Starting phenix.real_space_refine on Sat Sep 12 22:11:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n6i_23726/09_2026/7n6i_23726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n6i_23726/09_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_23726/09_2026/7n6i_23726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n6i_23726/09_2026/7n6i_23726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n6i_23726/09_2026/7n6i_23726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n6i_23726/09_2026/7n6i_23726.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7n6i_23726/09_2026/7n6i_23726.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n6i_23726/09_2026/7n6i_23726.cif" } 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-2.2.1-6174/lib/python3.11/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: 3.71, per 1000 atoms: 0.20 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: 1.43 Conformation dependent library (CDL) restraints added in 779.8 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: 1.77 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: 2.46 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 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: 25529 4.13 - 8.26: 578 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: 11329 31.41 - 62.81: 363 62.81 - 94.22: 63 94.22 - 125.63: 1 125.63 - 157.04: 3 Dihedral angle restraints: 11759 sinusoidal: 4935 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 11756 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.550 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 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= 1.323 Angle : 1.727 20.658 26167 Z= 1.363 Chirality : 0.127 1.733 2990 Planarity : 0.006 0.057 3205 Dihedral : 15.225 157.036 7339 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/Z covalent geometry : bond 0.01383 / 1.02 (19275) covalent geometry : angle 1.72719 / 1.36 (26167) hydrogen bonds : bond 0.22452 / 17.05 ( 903) hydrogen bonds : angle 7.07007 / 5.34 ( 2663) Misc. bond : bond 0.58402 / 28.87 ( 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 : 0.751 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: 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: 0.6875 (mp) REVERT: C 39 VAL cc_start: 0.8217 (t) cc_final: 0.7999 (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: 0.6829 (mt) REVERT: D 170 LEU cc_start: 0.8829 (tt) cc_final: 0.8627 (tt) REVERT: E 133 LEU cc_start: 0.8473 (mt) cc_final: 0.8248 (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: 0.7481 (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: 0.6314 (t70) REVERT: H 41 THR cc_start: 0.8869 (m) cc_final: 0.8588 (m) REVERT: H 163 ASP cc_start: 0.6463 (m-30) cc_final: 0.5808 (m-30) REVERT: I 77 HIS cc_start: 0.5999 (m-70) cc_final: 0.5779 (m-70) REVERT: I 204 PHE cc_start: 0.8420 (t80) cc_final: 0.7838 (t80) REVERT: J 211 TRP cc_start: 0.6531 (t-100) cc_final: 0.5895 (t-100) outliers start: 8 outliers final: 1 residues processed: 838 average time/residue: 0.1488 time to fit residues: 181.4826 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 : 0.755 ------------------------------------------------------------------------------- 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... 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 ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 J 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.108432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.076706 restraints weight = 61221.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.079312 restraints weight = 30976.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.081001 restraints weight = 20017.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.081969 restraints weight = 15117.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.082741 restraints weight = 12765.845| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19279 Z= 0.209 Angle : 0.812 13.464 26167 Z= 0.427 Chirality : 0.048 0.253 2990 Planarity : 0.006 0.059 3205 Dihedral : 14.670 158.128 3023 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.13 % Allowed : 17.52 % 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: 0.53 (0.17), residues: 2338 helix: 0.71 (0.14), residues: 1282 sheet: 0.07 (0.54), residues: 96 loop : 0.07 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 76 TYR 0.019 0.002 TYR C 115 PHE 0.039 0.003 PHE D 125 TRP 0.028 0.003 TRP H 45 HIS 0.007 0.002 HIS I 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (19275) covalent geometry : angle 0.81210 / 0.43 (26167) hydrogen bonds : bond 0.06745 / 5.14 ( 903) hydrogen bonds : angle 5.12082 / 3.86 ( 2663) Misc. bond : bond 0.00654 / 0.34 ( 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 491 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 417 time to evaluate : 0.685 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 29 LYS cc_start: 0.3557 (mmtt) cc_final: 0.3025 (mmtm) REVERT: C 183 ASP cc_start: 0.8666 (t0) cc_final: 0.8447 (t0) REVERT: C 187 LEU cc_start: 0.9233 (pp) cc_final: 0.8856 (tt) REVERT: C 229 MET cc_start: 0.5465 (ptp) cc_final: 0.5144 (pmm) REVERT: D 75 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8014 (t80) REVERT: D 159 ASP cc_start: 0.8055 (m-30) cc_final: 0.7663 (m-30) REVERT: D 170 LEU cc_start: 0.9255 (tt) cc_final: 0.8946 (tt) REVERT: D 187 LEU cc_start: 0.9249 (tp) cc_final: 0.8920 (tp) REVERT: D 210 MET cc_start: 0.8980 (ttt) cc_final: 0.8700 (ttt) REVERT: D 238 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8472 (tm-30) REVERT: D 250 GLU cc_start: 0.9348 (tt0) cc_final: 0.9037 (tt0) REVERT: E 55 SER cc_start: 0.8787 (m) cc_final: 0.8278 (p) REVERT: E 77 HIS cc_start: 0.7567 (m170) cc_final: 0.7366 (m-70) REVERT: E 99 LYS cc_start: 0.9353 (mmmm) cc_final: 0.9057 (mmtt) REVERT: E 152 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8471 (tp30) REVERT: E 204 PHE cc_start: 0.8836 (t80) cc_final: 0.8317 (t80) REVERT: E 210 MET cc_start: 0.8758 (mmt) cc_final: 0.8494 (mmm) REVERT: E 223 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8118 (p0) REVERT: E 246 GLU cc_start: 0.9358 (tp30) cc_final: 0.9038 (tp30) REVERT: F 38 GLN cc_start: 0.8221 (tp40) cc_final: 0.7450 (tp40) REVERT: F 45 TRP cc_start: 0.8752 (t60) cc_final: 0.8454 (t60) REVERT: F 62 SER cc_start: 0.8282 (m) cc_final: 0.7844 (t) REVERT: F 131 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8322 (mp0) REVERT: F 139 GLU cc_start: 0.8734 (mp0) cc_final: 0.8497 (mp0) REVERT: F 263 ILE cc_start: 0.7730 (mt) cc_final: 0.7495 (mm) REVERT: G 124 ASP cc_start: 0.8450 (t0) cc_final: 0.8174 (t0) REVERT: G 213 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7239 (tm-30) REVERT: G 229 MET cc_start: 0.9075 (mpp) cc_final: 0.8764 (pmm) REVERT: H 38 GLN cc_start: 0.8084 (tp40) cc_final: 0.7269 (tp40) REVERT: H 103 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8181 (ttmm) REVERT: H 159 ASP cc_start: 0.9241 (t0) cc_final: 0.8955 (t0) REVERT: H 195 ARG cc_start: 0.8053 (tpt170) cc_final: 0.7715 (ptt180) REVERT: H 207 THR cc_start: 0.9584 (m) cc_final: 0.9340 (p) REVERT: H 214 MET cc_start: 0.9225 (mtm) cc_final: 0.8843 (mpp) REVERT: H 246 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8622 (mp0) REVERT: I 38 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: I 140 MET cc_start: 0.7857 (tpp) cc_final: 0.7632 (tpp) REVERT: I 145 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8193 (mp0) REVERT: I 199 LEU cc_start: 0.7810 (tp) cc_final: 0.7183 (tp) REVERT: I 214 MET cc_start: 0.8952 (mtt) cc_final: 0.8721 (mtp) REVERT: I 224 LEU cc_start: 0.9313 (mt) cc_final: 0.8976 (mp) REVERT: I 229 MET cc_start: 0.9371 (mpp) cc_final: 0.8945 (pmm) REVERT: I 273 LYS cc_start: 0.9427 (mttt) cc_final: 0.8896 (tmtt) REVERT: J 38 GLN cc_start: 0.8651 (tp40) cc_final: 0.8439 (tp40) REVERT: J 93 TYR cc_start: 0.8131 (t80) cc_final: 0.7558 (t80) REVERT: J 116 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7251 (mtm-85) REVERT: J 267 VAL cc_start: 0.8906 (t) cc_final: 0.8340 (t) outliers start: 74 outliers final: 43 residues processed: 469 average time/residue: 0.1286 time to fit residues: 92.8154 Evaluate side-chains 375 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 328 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 245 ASP 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 221 SER Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 ASP 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 39 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 124 ASP 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 42 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 230 LEU 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 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 105 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 196 PHE 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: 7.9990 chunk 69 optimal weight: 5.9990 chunk 10 optimal weight: 40.0000 chunk 87 optimal weight: 0.0040 chunk 200 optimal weight: 7.9990 chunk 22 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 chunk 125 optimal weight: 0.1980 chunk 133 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN F 77 HIS G 43 HIS H 38 GLN I 38 GLN I 77 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.108765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.077069 restraints weight = 61178.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.079664 restraints weight = 31210.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.081381 restraints weight = 20359.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.082460 restraints weight = 15401.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.083062 restraints weight = 12907.996| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19279 Z= 0.150 Angle : 0.693 12.176 26167 Z= 0.361 Chirality : 0.044 0.306 2990 Planarity : 0.005 0.047 3205 Dihedral : 14.472 156.299 3021 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.46 % Allowed : 18.58 % Favored : 77.96 % 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: 0.82 (0.17), residues: 2338 helix: 0.99 (0.14), residues: 1292 sheet: -0.11 (0.51), residues: 96 loop : 0.16 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 258 TYR 0.022 0.002 TYR I 115 PHE 0.041 0.002 PHE I 125 TRP 0.036 0.002 TRP F 20 HIS 0.005 0.001 HIS J 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (19275) covalent geometry : angle 0.69325 / 0.36 (26167) hydrogen bonds : bond 0.05392 / 4.11 ( 903) hydrogen bonds : angle 4.75502 / 3.57 ( 2663) Misc. bond : bond 0.00235 / 0.12 ( 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 446 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 384 time to evaluate : 0.744 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: C 22 GLN cc_start: 0.9171 (mp10) cc_final: 0.8915 (pm20) REVERT: C 29 LYS cc_start: 0.2866 (mmtt) cc_final: 0.2623 (mmtm) REVERT: C 183 ASP cc_start: 0.8647 (t0) cc_final: 0.8356 (t0) REVERT: C 229 MET cc_start: 0.5425 (ptp) cc_final: 0.5122 (pmm) REVERT: D 55 SER cc_start: 0.8828 (m) cc_final: 0.8211 (p) REVERT: D 75 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8090 (t80) REVERT: D 159 ASP cc_start: 0.7941 (m-30) cc_final: 0.7521 (m-30) REVERT: D 170 LEU cc_start: 0.9273 (tt) cc_final: 0.8906 (tt) REVERT: D 187 LEU cc_start: 0.9233 (tp) cc_final: 0.8950 (tp) REVERT: D 207 THR cc_start: 0.9431 (m) cc_final: 0.9205 (p) REVERT: D 210 MET cc_start: 0.8942 (ttt) cc_final: 0.8605 (ttt) REVERT: D 229 MET cc_start: 0.8882 (mpp) cc_final: 0.8262 (pmm) REVERT: E 38 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7659 (tp40) REVERT: E 55 SER cc_start: 0.8823 (m) cc_final: 0.8381 (p) REVERT: E 77 HIS cc_start: 0.7638 (m170) cc_final: 0.7329 (m170) REVERT: E 145 GLU cc_start: 0.7787 (mp0) cc_final: 0.7264 (mp0) REVERT: E 150 LYS cc_start: 0.8947 (tptp) cc_final: 0.8715 (tptp) REVERT: E 246 GLU cc_start: 0.9347 (tp30) cc_final: 0.8912 (tp30) REVERT: F 45 TRP cc_start: 0.8786 (t60) cc_final: 0.8417 (t60) REVERT: F 55 SER cc_start: 0.9081 (p) cc_final: 0.8688 (p) REVERT: F 77 HIS cc_start: 0.6775 (m-70) cc_final: 0.6421 (m90) REVERT: F 139 GLU cc_start: 0.8808 (mp0) cc_final: 0.8420 (mp0) REVERT: F 188 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8280 (mm-30) REVERT: F 263 ILE cc_start: 0.7903 (mt) cc_final: 0.7685 (mm) REVERT: F 269 GLN cc_start: 0.8874 (mt0) cc_final: 0.8526 (mt0) REVERT: G 29 LYS cc_start: 0.9222 (pttp) cc_final: 0.8916 (pttm) REVERT: G 124 ASP cc_start: 0.8448 (t0) cc_final: 0.8129 (t0) REVERT: G 159 ASP cc_start: 0.8981 (m-30) cc_final: 0.8673 (m-30) REVERT: G 229 MET cc_start: 0.9041 (mpp) cc_final: 0.8628 (pmm) REVERT: H 28 LEU cc_start: 0.9619 (mm) cc_final: 0.9316 (mp) REVERT: H 159 ASP cc_start: 0.9067 (t0) cc_final: 0.7800 (t0) REVERT: H 162 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7368 (pp20) REVERT: H 163 ASP cc_start: 0.7688 (m-30) cc_final: 0.6888 (m-30) REVERT: H 195 ARG cc_start: 0.8138 (tpt170) cc_final: 0.7663 (ptt180) REVERT: H 214 MET cc_start: 0.9193 (mtm) cc_final: 0.8818 (mpp) REVERT: H 246 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8636 (mp0) REVERT: I 38 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8067 (tp40) REVERT: I 97 HIS cc_start: 0.8575 (m-70) cc_final: 0.8313 (m170) REVERT: I 140 MET cc_start: 0.7886 (tpp) cc_final: 0.7546 (tpp) REVERT: I 145 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8349 (mm-30) REVERT: I 156 ASP cc_start: 0.9516 (m-30) cc_final: 0.9213 (t0) REVERT: I 199 LEU cc_start: 0.7803 (tp) cc_final: 0.7153 (tp) REVERT: I 210 MET cc_start: 0.9298 (ttt) cc_final: 0.8942 (ttt) REVERT: I 224 LEU cc_start: 0.9293 (mt) cc_final: 0.8885 (mp) REVERT: I 229 MET cc_start: 0.9324 (mpp) cc_final: 0.8887 (pmm) REVERT: I 250 GLU cc_start: 0.9474 (tt0) cc_final: 0.9227 (mt-10) REVERT: I 273 LYS cc_start: 0.9410 (mttt) cc_final: 0.8876 (tmtt) REVERT: J 29 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8809 (tptt) REVERT: J 38 GLN cc_start: 0.8722 (tp40) cc_final: 0.8404 (tt0) REVERT: J 93 TYR cc_start: 0.8207 (t80) cc_final: 0.7614 (t80) REVERT: J 116 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7234 (mtm-85) outliers start: 62 outliers final: 30 residues processed: 426 average time/residue: 0.1242 time to fit residues: 82.0804 Evaluate side-chains 366 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 21 LEU 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 196 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 38 GLN 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 J residue 29 LYS Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 chunk 180 optimal weight: 0.3980 chunk 93 optimal weight: 0.6980 chunk 3 optimal weight: 40.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN F 213 GLN H 38 GLN I 38 GLN I 77 HIS I 185 GLN I 213 GLN ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.107251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075426 restraints weight = 60941.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.077971 restraints weight = 31248.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.079668 restraints weight = 20366.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.080733 restraints weight = 15363.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.081398 restraints weight = 12855.944| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19279 Z= 0.160 Angle : 0.673 15.639 26167 Z= 0.352 Chirality : 0.044 0.286 2990 Planarity : 0.004 0.041 3205 Dihedral : 14.414 155.954 3021 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.40 % Allowed : 19.14 % Favored : 77.46 % 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: 0.95 (0.17), residues: 2338 helix: 1.07 (0.14), residues: 1292 sheet: -0.02 (0.53), residues: 96 loop : 0.28 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 158 TYR 0.018 0.001 TYR F 112 PHE 0.055 0.003 PHE J 154 TRP 0.019 0.002 TRP F 20 HIS 0.010 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (19275) covalent geometry : angle 0.67337 / 0.35 (26167) hydrogen bonds : bond 0.05046 / 3.84 ( 903) hydrogen bonds : angle 4.76326 / 3.58 ( 2663) Misc. bond : bond 0.00147 / 0.07 ( 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 409 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 348 time to evaluate : 0.707 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 54 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8072 (tttt) REVERT: C 183 ASP cc_start: 0.8549 (t0) cc_final: 0.8309 (t0) REVERT: C 229 MET cc_start: 0.5534 (ptp) cc_final: 0.5231 (pmm) REVERT: D 29 LYS cc_start: 0.9323 (pttt) cc_final: 0.9094 (ptmt) REVERT: D 75 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8135 (t80) REVERT: D 140 MET cc_start: 0.7777 (ttm) cc_final: 0.7495 (mtp) REVERT: D 159 ASP cc_start: 0.8052 (m-30) cc_final: 0.7603 (m-30) REVERT: D 170 LEU cc_start: 0.9283 (tt) cc_final: 0.8873 (tt) REVERT: D 204 PHE cc_start: 0.8708 (t80) cc_final: 0.8396 (t80) REVERT: D 207 THR cc_start: 0.9482 (m) cc_final: 0.9259 (p) REVERT: D 210 MET cc_start: 0.8946 (ttt) cc_final: 0.8603 (ttt) REVERT: D 229 MET cc_start: 0.8815 (mpp) cc_final: 0.8186 (pmm) REVERT: D 246 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8533 (mp0) REVERT: D 250 GLU cc_start: 0.9294 (tt0) cc_final: 0.8822 (tt0) REVERT: E 38 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7815 (tp40) REVERT: E 55 SER cc_start: 0.8952 (m) cc_final: 0.8520 (p) REVERT: E 77 HIS cc_start: 0.7778 (m170) cc_final: 0.7369 (m-70) REVERT: E 145 GLU cc_start: 0.7789 (mp0) cc_final: 0.7305 (mp0) REVERT: E 229 MET cc_start: 0.8495 (mmm) cc_final: 0.8189 (mmt) REVERT: F 55 SER cc_start: 0.9132 (p) cc_final: 0.8766 (p) REVERT: F 77 HIS cc_start: 0.6996 (m-70) cc_final: 0.6616 (m-70) REVERT: F 139 GLU cc_start: 0.8863 (mp0) cc_final: 0.8403 (mp0) REVERT: F 188 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8424 (mm-30) REVERT: F 263 ILE cc_start: 0.8346 (mt) cc_final: 0.8029 (mm) REVERT: F 269 GLN cc_start: 0.9054 (mt0) cc_final: 0.8707 (mt0) REVERT: G 29 LYS cc_start: 0.9219 (pttp) cc_final: 0.8936 (pttm) REVERT: G 124 ASP cc_start: 0.8523 (t0) cc_final: 0.8201 (t0) REVERT: G 159 ASP cc_start: 0.9003 (m-30) cc_final: 0.8687 (m-30) REVERT: G 213 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7345 (tm-30) REVERT: G 214 MET cc_start: 0.8824 (mmm) cc_final: 0.7675 (mmm) REVERT: G 229 MET cc_start: 0.9164 (mpp) cc_final: 0.8633 (pmm) REVERT: H 159 ASP cc_start: 0.9104 (t0) cc_final: 0.7791 (t0) REVERT: H 162 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7411 (pp20) REVERT: H 163 ASP cc_start: 0.7675 (m-30) cc_final: 0.7040 (m-30) REVERT: H 195 ARG cc_start: 0.8296 (tpt170) cc_final: 0.7654 (ptt180) REVERT: H 210 MET cc_start: 0.9435 (mpp) cc_final: 0.9140 (mpp) REVERT: H 246 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8703 (mp0) REVERT: I 38 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8103 (tp40) REVERT: I 97 HIS cc_start: 0.8709 (m-70) cc_final: 0.8426 (m170) REVERT: I 145 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8340 (mm-30) REVERT: I 199 LEU cc_start: 0.7620 (tp) cc_final: 0.7063 (tp) REVERT: I 224 LEU cc_start: 0.9246 (mt) cc_final: 0.8988 (mp) REVERT: I 229 MET cc_start: 0.9325 (mpp) cc_final: 0.8864 (pmm) REVERT: I 273 LYS cc_start: 0.9436 (mttt) cc_final: 0.8967 (tmtt) REVERT: J 38 GLN cc_start: 0.8704 (tp40) cc_final: 0.8227 (tt0) outliers start: 61 outliers final: 39 residues processed: 387 average time/residue: 0.1231 time to fit residues: 75.8765 Evaluate side-chains 352 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 248 LEU 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 199 LEU 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 215 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 164 LEU 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 I residue 38 GLN 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 89 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 0.1980 chunk 25 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** 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 = 0.3846 r_free = 0.3846 target = 0.106689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075059 restraints weight = 61196.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.077499 restraints weight = 32061.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079092 restraints weight = 21145.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.080124 restraints weight = 16157.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.080768 restraints weight = 13581.779| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19279 Z= 0.146 Angle : 0.658 12.075 26167 Z= 0.340 Chirality : 0.044 0.289 2990 Planarity : 0.004 0.063 3205 Dihedral : 14.336 155.488 3021 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.18 % Allowed : 20.81 % Favored : 76.00 % 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 (0.17), residues: 2338 helix: 1.08 (0.14), residues: 1292 sheet: -0.02 (0.55), residues: 96 loop : 0.29 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 50 TYR 0.017 0.001 TYR F 112 PHE 0.036 0.002 PHE I 125 TRP 0.014 0.002 TRP D 20 HIS 0.005 0.001 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (19275) covalent geometry : angle 0.65780 / 0.34 (26167) hydrogen bonds : bond 0.04719 / 3.59 ( 903) hydrogen bonds : angle 4.69054 / 3.52 ( 2663) Misc. bond : bond 0.00147 / 0.07 ( 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 391 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 334 time to evaluate : 0.625 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: 0.8809 (mp10) cc_final: 0.8354 (pm20) REVERT: C 54 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8079 (tttt) REVERT: C 183 ASP cc_start: 0.8591 (t0) cc_final: 0.8319 (t0) REVERT: C 229 MET cc_start: 0.5517 (ptp) cc_final: 0.5197 (pmm) REVERT: D 29 LYS cc_start: 0.9313 (pttt) cc_final: 0.9092 (ptmt) REVERT: D 54 LYS cc_start: 0.9102 (mmpt) cc_final: 0.8774 (mmtt) REVERT: D 75 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.8106 (t80) REVERT: D 159 ASP cc_start: 0.8111 (m-30) cc_final: 0.7634 (m-30) REVERT: D 170 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8854 (tt) REVERT: D 204 PHE cc_start: 0.8744 (t80) cc_final: 0.8450 (t80) REVERT: D 210 MET cc_start: 0.8938 (ttt) cc_final: 0.8588 (ttt) REVERT: D 211 TRP cc_start: 0.9171 (t-100) cc_final: 0.8967 (t-100) REVERT: D 229 MET cc_start: 0.8827 (mpp) cc_final: 0.8170 (pmm) REVERT: D 246 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8484 (mp0) REVERT: D 250 GLU cc_start: 0.9277 (tt0) cc_final: 0.8796 (tt0) REVERT: E 38 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7632 (tp40) REVERT: E 55 SER cc_start: 0.8991 (m) cc_final: 0.8615 (p) REVERT: E 145 GLU cc_start: 0.7790 (mp0) cc_final: 0.7329 (mp0) REVERT: E 163 ASP cc_start: 0.7350 (p0) cc_final: 0.6825 (p0) REVERT: E 179 VAL cc_start: 0.9002 (t) cc_final: 0.8646 (p) REVERT: E 188 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7870 (mp0) REVERT: E 210 MET cc_start: 0.8884 (mmm) cc_final: 0.8608 (mpp) REVERT: E 229 MET cc_start: 0.8301 (mmm) cc_final: 0.8059 (mmm) REVERT: F 77 HIS cc_start: 0.6903 (m-70) cc_final: 0.6584 (m90) REVERT: F 139 GLU cc_start: 0.8843 (mp0) cc_final: 0.8429 (mp0) REVERT: F 144 ASP cc_start: 0.9018 (t0) cc_final: 0.8792 (t0) REVERT: F 188 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8430 (mm-30) REVERT: F 214 MET cc_start: 0.9186 (mmm) cc_final: 0.8695 (mmm) REVERT: F 229 MET cc_start: 0.8961 (pmm) cc_final: 0.8494 (pmm) REVERT: F 269 GLN cc_start: 0.9034 (mt0) cc_final: 0.8690 (mt0) REVERT: G 29 LYS cc_start: 0.9234 (pttp) cc_final: 0.9007 (pttm) REVERT: G 70 CYS cc_start: 0.9323 (m) cc_final: 0.9111 (m) REVERT: G 124 ASP cc_start: 0.8493 (t0) cc_final: 0.8153 (t0) REVERT: G 159 ASP cc_start: 0.8775 (m-30) cc_final: 0.8510 (m-30) REVERT: G 183 ASP cc_start: 0.8306 (t70) cc_final: 0.8082 (t0) REVERT: G 214 MET cc_start: 0.8502 (mmm) cc_final: 0.8179 (mmm) REVERT: G 229 MET cc_start: 0.9171 (mpp) cc_final: 0.8603 (pmm) REVERT: H 38 GLN cc_start: 0.8215 (tp40) cc_final: 0.7492 (tm-30) REVERT: H 54 LYS cc_start: 0.9020 (tptp) cc_final: 0.8598 (tptt) REVERT: H 140 MET cc_start: 0.8498 (pmm) cc_final: 0.8197 (pmm) REVERT: H 159 ASP cc_start: 0.9112 (t0) cc_final: 0.7871 (t0) REVERT: H 162 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7249 (pp20) REVERT: H 163 ASP cc_start: 0.7693 (m-30) cc_final: 0.6984 (m-30) REVERT: H 210 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.8962 (mpp) REVERT: H 214 MET cc_start: 0.9197 (mtm) cc_final: 0.8828 (mpp) REVERT: H 246 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8696 (mp0) REVERT: I 38 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: I 97 HIS cc_start: 0.8715 (m-70) cc_final: 0.8396 (m170) REVERT: I 145 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8349 (mm-30) REVERT: I 156 ASP cc_start: 0.9540 (OUTLIER) cc_final: 0.9227 (t0) REVERT: I 160 ILE cc_start: 0.9410 (mp) cc_final: 0.9141 (mp) REVERT: I 199 LEU cc_start: 0.7686 (tp) cc_final: 0.7132 (tp) REVERT: I 210 MET cc_start: 0.9189 (ttt) cc_final: 0.8987 (ttt) REVERT: I 224 LEU cc_start: 0.9282 (mt) cc_final: 0.9009 (mp) REVERT: I 229 MET cc_start: 0.9300 (mpp) cc_final: 0.8652 (pmm) REVERT: I 273 LYS cc_start: 0.9430 (mttt) cc_final: 0.8900 (tmtt) REVERT: J 38 GLN cc_start: 0.8723 (tp40) cc_final: 0.8258 (tt0) outliers start: 57 outliers final: 41 residues processed: 369 average time/residue: 0.1192 time to fit residues: 69.7885 Evaluate side-chains 362 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 THR 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 248 LEU 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 170 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 199 LEU 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 203 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 111 GLU 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 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 F residue 248 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 156 ASP 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 89 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain J residue 196 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 66 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 131 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 GLN E 223 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN H 37 GLN I 38 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 = 0.3813 r_free = 0.3813 target = 0.104564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072816 restraints weight = 61846.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.075238 restraints weight = 32236.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.076808 restraints weight = 21236.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077840 restraints weight = 16228.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.078397 restraints weight = 13676.785| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19279 Z= 0.188 Angle : 0.661 11.974 26167 Z= 0.347 Chirality : 0.044 0.383 2990 Planarity : 0.004 0.043 3205 Dihedral : 14.234 155.450 3021 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.19 % Allowed : 20.20 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2338 helix: 1.12 (0.15), residues: 1292 sheet: -0.05 (0.40), residues: 192 loop : 0.38 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 175 TYR 0.021 0.001 TYR F 112 PHE 0.047 0.002 PHE I 125 TRP 0.014 0.002 TRP D 20 HIS 0.006 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (19275) covalent geometry : angle 0.66060 / 0.35 (26167) hydrogen bonds : bond 0.04834 / 3.69 ( 903) hydrogen bonds : angle 4.74493 / 3.57 ( 2663) Misc. bond : bond 0.00194 / 0.10 ( 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 386 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 311 time to evaluate : 0.709 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: C 22 GLN cc_start: 0.8856 (mp10) cc_final: 0.8423 (pm20) REVERT: C 29 LYS cc_start: 0.3243 (mmtm) cc_final: 0.2819 (mmtp) REVERT: C 54 LYS cc_start: 0.8690 (mtpt) cc_final: 0.7959 (tttt) REVERT: C 183 ASP cc_start: 0.8682 (t0) cc_final: 0.8417 (t0) REVERT: C 229 MET cc_start: 0.5812 (ptp) cc_final: 0.5415 (pmm) REVERT: D 29 LYS cc_start: 0.9297 (pttt) cc_final: 0.9082 (ptmt) REVERT: D 75 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.8172 (t80) REVERT: D 159 ASP cc_start: 0.8197 (m-30) cc_final: 0.7702 (m-30) REVERT: D 170 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8911 (tt) REVERT: D 196 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8648 (t80) REVERT: D 210 MET cc_start: 0.8976 (ttt) cc_final: 0.8643 (ttt) REVERT: D 229 MET cc_start: 0.8931 (mpp) cc_final: 0.8215 (pmm) REVERT: D 246 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8458 (mp0) REVERT: D 250 GLU cc_start: 0.9283 (tt0) cc_final: 0.8810 (tt0) REVERT: E 38 GLN cc_start: 0.8648 (tp40) cc_final: 0.8297 (tp40) REVERT: E 55 SER cc_start: 0.9100 (m) cc_final: 0.8763 (p) REVERT: E 145 GLU cc_start: 0.7820 (mp0) cc_final: 0.7218 (mp0) REVERT: E 163 ASP cc_start: 0.7173 (p0) cc_final: 0.6627 (p0) REVERT: E 188 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7954 (mp0) REVERT: E 210 MET cc_start: 0.8967 (mmm) cc_final: 0.8741 (mmm) REVERT: F 134 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8659 (mtmm) REVERT: F 139 GLU cc_start: 0.8796 (mp0) cc_final: 0.8422 (mp0) REVERT: F 188 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8490 (mm-30) REVERT: G 124 ASP cc_start: 0.8559 (t0) cc_final: 0.8206 (t0) REVERT: G 159 ASP cc_start: 0.8833 (m-30) cc_final: 0.8492 (m-30) REVERT: G 229 MET cc_start: 0.9223 (mpp) cc_final: 0.8610 (pmm) REVERT: G 268 LEU cc_start: 0.9419 (mt) cc_final: 0.9160 (tp) REVERT: H 54 LYS cc_start: 0.8758 (tptp) cc_final: 0.8482 (tptt) REVERT: H 100 CYS cc_start: 0.8105 (t) cc_final: 0.7885 (t) REVERT: H 104 ASP cc_start: 0.8652 (t0) cc_final: 0.8058 (t0) REVERT: H 140 MET cc_start: 0.8400 (pmm) cc_final: 0.8126 (pmm) REVERT: H 159 ASP cc_start: 0.9153 (t0) cc_final: 0.8523 (t0) REVERT: H 163 ASP cc_start: 0.7798 (m-30) cc_final: 0.7495 (m-30) REVERT: H 210 MET cc_start: 0.9413 (mpp) cc_final: 0.8997 (mpp) REVERT: H 214 MET cc_start: 0.9247 (mtm) cc_final: 0.8839 (mpp) REVERT: H 246 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8572 (mp0) REVERT: I 38 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8223 (tp40) REVERT: I 97 HIS cc_start: 0.8652 (m-70) cc_final: 0.8365 (m170) REVERT: I 145 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8448 (mm-30) REVERT: I 156 ASP cc_start: 0.9486 (OUTLIER) cc_final: 0.9207 (t0) REVERT: I 160 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9119 (mp) REVERT: I 199 LEU cc_start: 0.7666 (tp) cc_final: 0.6963 (tp) REVERT: I 229 MET cc_start: 0.9369 (mpp) cc_final: 0.8794 (pmm) REVERT: I 273 LYS cc_start: 0.9485 (mttt) cc_final: 0.8978 (tmtt) REVERT: J 38 GLN cc_start: 0.8678 (tp40) cc_final: 0.8433 (tt0) REVERT: J 210 MET cc_start: 0.9693 (ptp) cc_final: 0.9480 (mpp) REVERT: J 224 LEU cc_start: 0.9158 (mt) cc_final: 0.8912 (mt) REVERT: J 229 MET cc_start: 0.9073 (ptp) cc_final: 0.8537 (ppp) REVERT: J 246 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8870 (mm-30) outliers start: 75 outliers final: 56 residues processed: 362 average time/residue: 0.1258 time to fit residues: 72.6142 Evaluate side-chains 362 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 300 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 118 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 179 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 232 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 64 THR 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 196 PHE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 256 LEU 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 203 ASP Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 111 GLU 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 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 F residue 248 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 176 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 133 LEU Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 160 ILE 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 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain J residue 196 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 40.0000 chunk 213 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 164 optimal weight: 0.1980 chunk 200 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 142 optimal weight: 0.0570 chunk 176 optimal weight: 8.9990 overall best weight: 1.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN D 38 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN J 97 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.104444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072919 restraints weight = 62721.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075237 restraints weight = 33803.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.076746 restraints weight = 22778.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.077736 restraints weight = 17605.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.078248 restraints weight = 15021.083| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.6077 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 : 0.671 10.800 26167 Z= 0.347 Chirality : 0.045 0.269 2990 Planarity : 0.004 0.040 3205 Dihedral : 14.160 155.270 3021 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.69 % Allowed : 20.20 % Favored : 75.11 % 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: 1.03 (0.17), residues: 2338 helix: 1.13 (0.14), residues: 1292 sheet: -0.03 (0.40), residues: 192 loop : 0.36 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 85 TYR 0.019 0.001 TYR F 112 PHE 0.040 0.002 PHE I 125 TRP 0.030 0.002 TRP D 20 HIS 0.006 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (19275) covalent geometry : angle 0.67071 / 0.35 (26167) hydrogen bonds : bond 0.04597 / 3.52 ( 903) hydrogen bonds : angle 4.70008 / 3.53 ( 2663) Misc. bond : bond 0.00163 / 0.08 ( 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 397 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 313 time to evaluate : 0.928 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: C 29 LYS cc_start: 0.3098 (mmtm) cc_final: 0.2796 (mmtp) REVERT: C 54 LYS cc_start: 0.8696 (mtpt) cc_final: 0.7942 (tttt) REVERT: C 131 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8464 (tm-30) REVERT: C 183 ASP cc_start: 0.8644 (t0) cc_final: 0.8373 (t0) REVERT: C 229 MET cc_start: 0.5915 (ptp) cc_final: 0.5474 (pmm) REVERT: D 38 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8610 (mp10) REVERT: D 75 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8172 (t80) REVERT: D 159 ASP cc_start: 0.8187 (m-30) cc_final: 0.7663 (m-30) REVERT: D 170 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8951 (tt) REVERT: D 196 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8015 (t80) REVERT: D 210 MET cc_start: 0.8987 (ttt) cc_final: 0.8688 (ttt) REVERT: D 229 MET cc_start: 0.9056 (mpp) cc_final: 0.7935 (ptp) REVERT: D 246 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8415 (mp0) REVERT: D 250 GLU cc_start: 0.9244 (tt0) cc_final: 0.8800 (tt0) REVERT: E 55 SER cc_start: 0.9105 (m) cc_final: 0.8786 (p) REVERT: E 145 GLU cc_start: 0.7810 (mp0) cc_final: 0.7248 (mp0) REVERT: E 188 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7965 (mp0) REVERT: F 77 HIS cc_start: 0.6997 (m-70) cc_final: 0.6707 (m-70) REVERT: F 134 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8607 (mtmm) REVERT: F 139 GLU cc_start: 0.8708 (mp0) cc_final: 0.8392 (mp0) REVERT: F 185 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8110 (mm-40) REVERT: F 188 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8521 (mm-30) REVERT: F 229 MET cc_start: 0.8973 (pmm) cc_final: 0.8415 (pmm) REVERT: G 124 ASP cc_start: 0.8524 (t0) cc_final: 0.8178 (t0) REVERT: G 159 ASP cc_start: 0.8758 (m-30) cc_final: 0.8400 (m-30) REVERT: G 229 MET cc_start: 0.9197 (mpp) cc_final: 0.8786 (pmm) REVERT: G 268 LEU cc_start: 0.9431 (mt) cc_final: 0.9210 (tp) REVERT: H 54 LYS cc_start: 0.8853 (tptp) cc_final: 0.8509 (tptt) REVERT: H 140 MET cc_start: 0.8416 (pmm) cc_final: 0.8156 (pmm) REVERT: H 159 ASP cc_start: 0.9129 (t0) cc_final: 0.8552 (t0) REVERT: H 163 ASP cc_start: 0.7784 (m-30) cc_final: 0.7476 (m-30) REVERT: H 214 MET cc_start: 0.9227 (mtm) cc_final: 0.9025 (mtm) REVERT: H 246 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8543 (mp0) REVERT: I 38 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: I 70 CYS cc_start: 0.8879 (m) cc_final: 0.8651 (p) REVERT: I 97 HIS cc_start: 0.8643 (m-70) cc_final: 0.8429 (m-70) REVERT: I 107 LYS cc_start: 0.9415 (ptmm) cc_final: 0.9195 (pptt) REVERT: I 145 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8492 (mm-30) REVERT: I 156 ASP cc_start: 0.9417 (OUTLIER) cc_final: 0.9170 (t0) REVERT: I 160 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9094 (mp) REVERT: I 199 LEU cc_start: 0.7746 (tp) cc_final: 0.6968 (tp) REVERT: I 213 GLN cc_start: 0.9150 (mm110) cc_final: 0.8895 (mp10) REVERT: I 229 MET cc_start: 0.9326 (mpp) cc_final: 0.8822 (pmm) REVERT: I 273 LYS cc_start: 0.9493 (mttt) cc_final: 0.8932 (tmtt) REVERT: J 38 GLN cc_start: 0.8734 (tp40) cc_final: 0.8434 (tt0) REVERT: J 224 LEU cc_start: 0.9148 (mt) cc_final: 0.8924 (mt) REVERT: J 229 MET cc_start: 0.9090 (ptp) cc_final: 0.8580 (ppp) REVERT: J 246 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8879 (mm-30) outliers start: 84 outliers final: 57 residues processed: 365 average time/residue: 0.1278 time to fit residues: 74.1196 Evaluate side-chains 359 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 295 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU 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 179 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 245 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 64 THR 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 196 PHE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 31 LYS 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 213 GLN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 111 GLU 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 179 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 233 LEU 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 133 LEU Chi-restraints excluded: chain I residue 156 ASP 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 248 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 131 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.104172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073015 restraints weight = 62821.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075283 restraints weight = 33955.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.076776 restraints weight = 22901.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077677 restraints weight = 17739.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.078319 restraints weight = 15156.366| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6259 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= 0.153 Angle : 0.687 12.144 26167 Z= 0.354 Chirality : 0.045 0.304 2990 Planarity : 0.004 0.041 3205 Dihedral : 14.107 155.308 3021 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.85 % Allowed : 21.76 % Favored : 74.39 % 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: 0.98 (0.17), residues: 2338 helix: 1.10 (0.14), residues: 1292 sheet: -0.06 (0.40), residues: 192 loop : 0.33 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 27 TYR 0.020 0.001 TYR J 75 PHE 0.045 0.002 PHE I 125 TRP 0.017 0.002 TRP J 211 HIS 0.005 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (19275) covalent geometry : angle 0.68724 / 0.35 (26167) hydrogen bonds : bond 0.04487 / 3.42 ( 903) hydrogen bonds : angle 4.72817 / 3.57 ( 2663) Misc. bond : bond 0.00154 / 0.08 ( 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 373 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 304 time to evaluate : 0.716 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: C 29 LYS cc_start: 0.3139 (mmtm) cc_final: 0.2925 (mmtm) REVERT: C 131 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8421 (tm-30) REVERT: C 183 ASP cc_start: 0.8640 (t0) cc_final: 0.8370 (t0) REVERT: C 210 MET cc_start: 0.8691 (ptm) cc_final: 0.8478 (ptp) REVERT: C 229 MET cc_start: 0.6187 (ptp) cc_final: 0.5701 (pmm) REVERT: D 38 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8606 (mp10) REVERT: D 75 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8169 (t80) REVERT: D 159 ASP cc_start: 0.8227 (m-30) cc_final: 0.7689 (m-30) REVERT: D 196 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.7923 (t80) REVERT: D 210 MET cc_start: 0.9023 (ttt) cc_final: 0.8737 (ttt) REVERT: D 229 MET cc_start: 0.9051 (mpp) cc_final: 0.8526 (mmt) REVERT: D 250 GLU cc_start: 0.9258 (tt0) cc_final: 0.8834 (tt0) REVERT: E 55 SER cc_start: 0.9109 (m) cc_final: 0.8807 (p) REVERT: E 145 GLU cc_start: 0.7806 (mp0) cc_final: 0.7249 (mp0) REVERT: E 163 ASP cc_start: 0.7197 (p0) cc_final: 0.6666 (p0) REVERT: E 188 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7927 (mp0) REVERT: E 210 MET cc_start: 0.8889 (mmm) cc_final: 0.8580 (mpp) REVERT: F 134 LYS cc_start: 0.8869 (mtmm) cc_final: 0.8635 (mtmm) REVERT: F 139 GLU cc_start: 0.8701 (mp0) cc_final: 0.8385 (mp0) REVERT: F 159 ASP cc_start: 0.8029 (t70) cc_final: 0.7783 (t0) REVERT: F 185 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8148 (mm-40) REVERT: F 188 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8532 (mm-30) REVERT: F 229 MET cc_start: 0.8962 (pmm) cc_final: 0.8481 (pmm) REVERT: G 124 ASP cc_start: 0.8500 (t0) cc_final: 0.8158 (t0) REVERT: G 159 ASP cc_start: 0.8752 (m-30) cc_final: 0.8337 (m-30) REVERT: G 214 MET cc_start: 0.8838 (mmm) cc_final: 0.8547 (mmm) REVERT: G 229 MET cc_start: 0.9196 (mpp) cc_final: 0.8782 (pmm) REVERT: G 268 LEU cc_start: 0.9443 (mt) cc_final: 0.9234 (tp) REVERT: H 54 LYS cc_start: 0.8943 (tptp) cc_final: 0.8509 (tptt) REVERT: H 140 MET cc_start: 0.8431 (pmm) cc_final: 0.8172 (pmm) REVERT: H 159 ASP cc_start: 0.9105 (t0) cc_final: 0.8533 (t0) REVERT: H 163 ASP cc_start: 0.7822 (m-30) cc_final: 0.7508 (m-30) REVERT: H 214 MET cc_start: 0.9232 (mtm) cc_final: 0.8793 (mpp) REVERT: H 246 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8564 (mp0) REVERT: I 38 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: I 70 CYS cc_start: 0.8882 (m) cc_final: 0.8657 (p) REVERT: I 97 HIS cc_start: 0.8640 (m-70) cc_final: 0.8414 (m-70) REVERT: I 107 LYS cc_start: 0.9413 (ptmm) cc_final: 0.9172 (pptt) REVERT: I 145 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8507 (mm-30) REVERT: I 156 ASP cc_start: 0.9354 (OUTLIER) cc_final: 0.9059 (t0) REVERT: I 160 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9047 (mp) REVERT: I 199 LEU cc_start: 0.7774 (tp) cc_final: 0.6960 (tp) REVERT: I 229 MET cc_start: 0.9331 (mpp) cc_final: 0.8866 (pmm) REVERT: I 273 LYS cc_start: 0.9499 (mttt) cc_final: 0.8940 (tmtt) REVERT: J 38 GLN cc_start: 0.8750 (tp40) cc_final: 0.8448 (tt0) REVERT: J 224 LEU cc_start: 0.9078 (mt) cc_final: 0.8863 (mt) REVERT: J 229 MET cc_start: 0.9103 (ptp) cc_final: 0.8557 (ppp) REVERT: J 246 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8884 (mm-30) outliers start: 69 outliers final: 50 residues processed: 348 average time/residue: 0.1260 time to fit residues: 69.6457 Evaluate side-chains 351 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 64 THR 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 183 ASP Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 31 LYS 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 213 GLN Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 111 GLU 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 179 VAL Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 176 LEU 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 I residue 38 GLN Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 156 ASP 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 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 105 LEU Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 129 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 85 optimal weight: 0.0970 chunk 180 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 19 optimal weight: 30.0000 chunk 189 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS J 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.104066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072412 restraints weight = 62789.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074674 restraints weight = 34127.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076143 restraints weight = 23140.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.077077 restraints weight = 18042.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.077573 restraints weight = 15442.248| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.6421 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= 0.150 Angle : 0.707 12.505 26167 Z= 0.361 Chirality : 0.045 0.304 2990 Planarity : 0.004 0.041 3205 Dihedral : 14.003 155.378 3019 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.63 % Allowed : 22.32 % Favored : 74.05 % 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: 0.97 (0.17), residues: 2338 helix: 1.10 (0.15), residues: 1292 sheet: -0.08 (0.40), residues: 192 loop : 0.32 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 231 TYR 0.019 0.001 TYR H 275 PHE 0.043 0.002 PHE I 125 TRP 0.017 0.001 TRP J 211 HIS 0.012 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (19275) covalent geometry : angle 0.70707 / 0.36 (26167) hydrogen bonds : bond 0.04395 / 3.34 ( 903) hydrogen bonds : angle 4.73392 / 3.58 ( 2663) Misc. bond : bond 0.00147 / 0.07 ( 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 371 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 306 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: C 29 LYS cc_start: 0.3144 (mmtm) cc_final: 0.2913 (mmtm) REVERT: C 131 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8414 (tm-30) REVERT: C 183 ASP cc_start: 0.8652 (t0) cc_final: 0.8363 (t0) REVERT: C 210 MET cc_start: 0.8723 (ptm) cc_final: 0.8517 (ptp) REVERT: C 229 MET cc_start: 0.5976 (ptp) cc_final: 0.5506 (pmm) REVERT: D 75 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8161 (t80) REVERT: D 145 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8340 (mm-30) REVERT: D 159 ASP cc_start: 0.8158 (m-30) cc_final: 0.7644 (m-30) REVERT: D 196 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.7912 (t80) REVERT: D 210 MET cc_start: 0.9035 (ttt) cc_final: 0.8759 (ttt) REVERT: D 229 MET cc_start: 0.8893 (mpp) cc_final: 0.7876 (ptp) REVERT: D 250 GLU cc_start: 0.9271 (tt0) cc_final: 0.8847 (tt0) REVERT: E 55 SER cc_start: 0.9119 (m) cc_final: 0.8830 (p) REVERT: E 145 GLU cc_start: 0.7812 (mp0) cc_final: 0.7268 (mp0) REVERT: E 163 ASP cc_start: 0.7207 (p0) cc_final: 0.6685 (p0) REVERT: E 210 MET cc_start: 0.8878 (mmm) cc_final: 0.8663 (mpp) REVERT: E 238 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8425 (mp0) REVERT: F 127 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8108 (p0) REVERT: F 134 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8677 (mtmm) REVERT: F 139 GLU cc_start: 0.8698 (mp0) cc_final: 0.8388 (mp0) REVERT: F 159 ASP cc_start: 0.8041 (t70) cc_final: 0.7803 (t0) REVERT: F 185 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8143 (mm-40) REVERT: F 214 MET cc_start: 0.9216 (mmm) cc_final: 0.8941 (mmp) REVERT: F 229 MET cc_start: 0.8950 (pmm) cc_final: 0.8489 (pmm) REVERT: G 124 ASP cc_start: 0.8512 (t0) cc_final: 0.8167 (t0) REVERT: G 159 ASP cc_start: 0.8701 (m-30) cc_final: 0.8316 (m-30) REVERT: G 214 MET cc_start: 0.8824 (mmm) cc_final: 0.8561 (mmm) REVERT: G 229 MET cc_start: 0.9201 (mpp) cc_final: 0.8779 (pmm) REVERT: G 268 LEU cc_start: 0.9455 (mt) cc_final: 0.9247 (tp) REVERT: H 54 LYS cc_start: 0.8942 (tptp) cc_final: 0.8490 (tptt) REVERT: H 78 LYS cc_start: 0.7179 (mmmt) cc_final: 0.6534 (ttpp) REVERT: H 140 MET cc_start: 0.8450 (pmm) cc_final: 0.8174 (pmm) REVERT: H 214 MET cc_start: 0.9223 (mtm) cc_final: 0.8784 (mpp) REVERT: H 246 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8731 (mp0) REVERT: I 97 HIS cc_start: 0.8623 (m-70) cc_final: 0.8317 (m170) REVERT: I 107 LYS cc_start: 0.9419 (ptmm) cc_final: 0.9171 (pptt) REVERT: I 140 MET cc_start: 0.7680 (tpp) cc_final: 0.7441 (mpp) REVERT: I 145 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8506 (mm-30) REVERT: I 156 ASP cc_start: 0.9347 (OUTLIER) cc_final: 0.9040 (t0) REVERT: I 160 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9008 (mp) REVERT: I 199 LEU cc_start: 0.7808 (tp) cc_final: 0.7018 (tp) REVERT: I 229 MET cc_start: 0.9363 (mpp) cc_final: 0.8893 (pmm) REVERT: I 273 LYS cc_start: 0.9511 (mttt) cc_final: 0.8943 (tmtt) REVERT: J 38 GLN cc_start: 0.8734 (tp40) cc_final: 0.8438 (tt0) REVERT: J 224 LEU cc_start: 0.9084 (mt) cc_final: 0.8875 (mt) REVERT: J 229 MET cc_start: 0.9113 (ptp) cc_final: 0.8571 (ppp) REVERT: J 246 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8880 (mm-30) outliers start: 65 outliers final: 45 residues processed: 347 average time/residue: 0.1249 time to fit residues: 68.9023 Evaluate side-chains 345 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 232 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 64 THR 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 183 ASP Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 256 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 213 GLN Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 111 GLU 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 179 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 176 LEU 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 I residue 133 LEU Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 160 ILE 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 168 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 171 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 52 optimal weight: 0.0870 chunk 138 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.104801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.072830 restraints weight = 63234.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075201 restraints weight = 33791.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076736 restraints weight = 22664.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077704 restraints weight = 17544.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078296 restraints weight = 14961.223| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 19279 Z= 0.131 Angle : 0.716 13.480 26167 Z= 0.363 Chirality : 0.045 0.452 2990 Planarity : 0.004 0.042 3205 Dihedral : 13.925 155.334 3019 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.57 % Allowed : 23.10 % Favored : 74.33 % 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 (0.18), residues: 2338 helix: 1.05 (0.15), residues: 1300 sheet: -0.06 (0.40), residues: 192 loop : 0.26 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 231 TYR 0.022 0.001 TYR J 75 PHE 0.044 0.002 PHE I 125 TRP 0.017 0.001 TRP J 211 HIS 0.007 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (19275) covalent geometry : angle 0.71577 / 0.36 (26167) hydrogen bonds : bond 0.04169 / 3.16 ( 903) hydrogen bonds : angle 4.72283 / 3.57 ( 2663) Misc. bond : bond 0.00119 / 0.06 ( 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 356 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 310 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3375 (mmtm) cc_final: 0.3041 (mmtp) REVERT: C 183 ASP cc_start: 0.8613 (t0) cc_final: 0.8310 (t0) REVERT: C 210 MET cc_start: 0.8662 (ptm) cc_final: 0.8457 (ptp) REVERT: C 229 MET cc_start: 0.5962 (ptp) cc_final: 0.5489 (pmm) REVERT: D 37 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8828 (pp30) REVERT: D 38 GLN cc_start: 0.9192 (mp10) cc_final: 0.8861 (tt0) REVERT: D 75 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8203 (t80) REVERT: D 140 MET cc_start: 0.7934 (mtp) cc_final: 0.7722 (ttm) REVERT: D 145 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8357 (mm-30) REVERT: D 159 ASP cc_start: 0.8180 (m-30) cc_final: 0.7658 (m-30) REVERT: D 199 LEU cc_start: 0.9067 (mm) cc_final: 0.8738 (mm) REVERT: D 210 MET cc_start: 0.9052 (ttt) cc_final: 0.8757 (ttt) REVERT: D 229 MET cc_start: 0.8961 (mpp) cc_final: 0.7784 (ptp) REVERT: D 250 GLU cc_start: 0.9258 (tt0) cc_final: 0.8835 (tt0) REVERT: E 55 SER cc_start: 0.9109 (m) cc_final: 0.8796 (p) REVERT: E 145 GLU cc_start: 0.7802 (mp0) cc_final: 0.7402 (mp0) REVERT: E 163 ASP cc_start: 0.7297 (p0) cc_final: 0.6803 (p0) REVERT: E 179 VAL cc_start: 0.9041 (t) cc_final: 0.8675 (p) REVERT: E 185 GLN cc_start: 0.7834 (tp-100) cc_final: 0.7434 (tp-100) REVERT: E 238 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8438 (mp0) REVERT: F 80 GLN cc_start: 0.6418 (mm-40) cc_final: 0.6112 (mm-40) REVERT: F 125 PHE cc_start: 0.9263 (m-80) cc_final: 0.8909 (m-80) REVERT: F 139 GLU cc_start: 0.8668 (mp0) cc_final: 0.8360 (mp0) REVERT: F 159 ASP cc_start: 0.8038 (t70) cc_final: 0.7805 (t0) REVERT: F 185 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8111 (mm-40) REVERT: F 214 MET cc_start: 0.9198 (mmm) cc_final: 0.8899 (mmp) REVERT: F 229 MET cc_start: 0.8962 (pmm) cc_final: 0.8498 (pmm) REVERT: G 124 ASP cc_start: 0.8478 (t0) cc_final: 0.8123 (t0) REVERT: G 159 ASP cc_start: 0.8651 (m-30) cc_final: 0.8272 (m-30) REVERT: G 214 MET cc_start: 0.8773 (mmm) cc_final: 0.8563 (mmm) REVERT: G 229 MET cc_start: 0.9183 (mpp) cc_final: 0.8770 (pmm) REVERT: G 268 LEU cc_start: 0.9460 (mt) cc_final: 0.9248 (tp) REVERT: H 54 LYS cc_start: 0.8938 (tptp) cc_final: 0.8449 (tptt) REVERT: H 78 LYS cc_start: 0.7080 (mmmt) cc_final: 0.6565 (ttpp) REVERT: H 103 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8252 (ttmm) REVERT: H 140 MET cc_start: 0.8365 (pmm) cc_final: 0.8110 (pmm) REVERT: H 159 ASP cc_start: 0.9111 (t0) cc_final: 0.8638 (t0) REVERT: H 163 ASP cc_start: 0.7799 (m-30) cc_final: 0.7518 (m-30) REVERT: H 214 MET cc_start: 0.9205 (mtm) cc_final: 0.8827 (mtm) REVERT: H 246 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8718 (mp0) REVERT: I 38 GLN cc_start: 0.8673 (mp10) cc_final: 0.8338 (mm-40) REVERT: I 97 HIS cc_start: 0.8583 (m-70) cc_final: 0.8338 (m170) REVERT: I 107 LYS cc_start: 0.9419 (ptmm) cc_final: 0.9160 (pptt) REVERT: I 140 MET cc_start: 0.7806 (tpp) cc_final: 0.7530 (mpp) REVERT: I 145 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8493 (mm-30) REVERT: I 156 ASP cc_start: 0.9305 (OUTLIER) cc_final: 0.9097 (t0) REVERT: I 160 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8925 (mp) REVERT: I 199 LEU cc_start: 0.7939 (tp) cc_final: 0.7156 (tp) REVERT: I 229 MET cc_start: 0.9344 (mpp) cc_final: 0.8874 (pmm) REVERT: I 273 LYS cc_start: 0.9501 (mttt) cc_final: 0.8942 (tmtt) REVERT: J 38 GLN cc_start: 0.8729 (tp40) cc_final: 0.8204 (tt0) REVERT: J 211 TRP cc_start: 0.9182 (t-100) cc_final: 0.8751 (t-100) REVERT: J 224 LEU cc_start: 0.9089 (mt) cc_final: 0.8869 (mt) REVERT: J 229 MET cc_start: 0.9115 (ptp) cc_final: 0.8500 (ppp) REVERT: J 230 LEU cc_start: 0.9817 (tt) cc_final: 0.9597 (mt) outliers start: 46 outliers final: 36 residues processed: 342 average time/residue: 0.1316 time to fit residues: 71.0534 Evaluate side-chains 342 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 64 THR 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 E residue 64 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 111 GLU 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 199 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 227 LYS 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 168 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 193 optimal weight: 0.9990 chunk 189 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 14 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.104797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073302 restraints weight = 63407.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075577 restraints weight = 34310.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.077119 restraints weight = 23176.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.078056 restraints weight = 17923.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078564 restraints weight = 15291.997| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.6648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 19279 Z= 0.128 Angle : 0.724 21.164 26167 Z= 0.365 Chirality : 0.045 0.325 2990 Planarity : 0.004 0.042 3205 Dihedral : 13.852 155.376 3019 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.46 % Allowed : 23.21 % Favored : 74.33 % 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: 0.85 (0.18), residues: 2338 helix: 1.01 (0.15), residues: 1304 sheet: -0.03 (0.40), residues: 192 loop : 0.21 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 231 TYR 0.017 0.001 TYR J 93 PHE 0.045 0.002 PHE I 125 TRP 0.035 0.002 TRP G 211 HIS 0.007 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (19275) covalent geometry : angle 0.72369 / 0.36 (26167) hydrogen bonds : bond 0.04048 / 3.06 ( 903) hydrogen bonds : angle 4.73960 / 3.58 ( 2663) Misc. bond : bond 0.00114 / 0.06 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3694.15 seconds wall clock time: 64 minutes 20.52 seconds (3860.52 seconds total)