Starting phenix.real_space_refine on Sat Jul 4 05:52:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n6i_23726/07_2026/7n6i_23726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n6i_23726/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7n6i_23726/07_2026/7n6i_23726.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n6i_23726/07_2026/7n6i_23726.cif" model { file = "/net/cci-nas-00/data/ceres_data/7n6i_23726/07_2026/7n6i_23726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n6i_23726/07_2026/7n6i_23726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n6i_23726/07_2026/7n6i_23726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n6i_23726/07_2026/7n6i_23726.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 Mg 7 5.21 5 S 64 5.16 5 C 11744 2.51 5 N 3472 2.21 5 O 3597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 4.20, per 1000 atoms: 0.22 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: 1.89 Conformation dependent library (CDL) restraints added in 774.7 milliseconds 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 16 sheets defined 57.7% alpha, 4.3% beta 14 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.13 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: 2.85 Time building geometry restraints manager: 2.39 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.780 Find NCS groups from input model: 0.430 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- 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 1.72690 / 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 : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LEU cc_start: 0.7135 (mt) cc_final: 0.6876 (mp) REVERT: C 39 VAL cc_start: 0.8217 (t) cc_final: 0.8000 (t) REVERT: C 42 LEU cc_start: 0.9103 (tp) cc_final: 0.8580 (tp) REVERT: C 194 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8253 (tt) REVERT: C 199 LEU cc_start: 0.7136 (mt) cc_final: 0.6831 (mt) REVERT: D 170 LEU cc_start: 0.8829 (tt) cc_final: 0.8628 (tt) REVERT: E 133 LEU cc_start: 0.8473 (mt) cc_final: 0.8249 (mt) REVERT: E 240 TYR cc_start: 0.8769 (m-80) cc_final: 0.8497 (m-80) REVERT: F 38 GLN cc_start: 0.7982 (tp40) cc_final: 0.7619 (tp40) REVERT: F 70 CYS cc_start: 0.7889 (m) cc_final: 0.7480 (m) REVERT: F 164 LEU cc_start: 0.8028 (mt) cc_final: 0.7790 (mt) REVERT: F 183 ASP cc_start: 0.6544 (t70) cc_final: 0.6313 (t70) REVERT: H 41 THR cc_start: 0.8869 (m) cc_final: 0.8589 (m) REVERT: H 163 ASP cc_start: 0.6463 (m-30) cc_final: 0.5805 (m-30) REVERT: I 77 HIS cc_start: 0.5999 (m-70) cc_final: 0.5776 (m-70) REVERT: I 204 PHE cc_start: 0.8420 (t80) cc_final: 0.7838 (t80) REVERT: J 100 CYS cc_start: 0.1713 (t) cc_final: 0.1494 (t) REVERT: J 211 TRP cc_start: 0.6531 (t-100) cc_final: 0.5893 (t-100) outliers start: 8 outliers final: 1 residues processed: 838 average time/residue: 0.1520 time to fit residues: 185.1969 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 : 0.517 ------------------------------------------------------------------------------- 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** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 HIS ** 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 = 0.3872 r_free = 0.3872 target = 0.108550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.076750 restraints weight = 61175.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.079382 restraints weight = 30917.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.081104 restraints weight = 19974.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.082188 restraints weight = 15048.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.082879 restraints weight = 12601.098| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19279 Z= 0.213 Angle : 0.807 16.106 26167 Z= 0.425 Chirality : 0.047 0.296 2990 Planarity : 0.006 0.056 3205 Dihedral : 14.671 159.153 3023 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.52 % Allowed : 18.53 % 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: 0.54 (0.16), residues: 2338 helix: 0.72 (0.14), residues: 1282 sheet: 0.06 (0.54), residues: 96 loop : 0.07 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 76 TYR 0.019 0.002 TYR D 73 PHE 0.038 0.003 PHE D 125 TRP 0.028 0.003 TRP H 45 HIS 0.008 0.001 HIS I 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (19275) covalent geometry : angle 0.80738 / 0.43 (26167) hydrogen bonds : bond 0.07205 / 5.49 ( 903) hydrogen bonds : angle 5.21005 / 3.93 ( 2663) Misc. bond : bond 0.00614 / 0.32 ( 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 478 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 415 time to evaluate : 0.766 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 115 TYR cc_start: 0.8963 (m-80) cc_final: 0.8740 (m-10) REVERT: C 183 ASP cc_start: 0.8672 (t0) cc_final: 0.8459 (t0) REVERT: C 187 LEU cc_start: 0.9253 (pp) cc_final: 0.8907 (tt) REVERT: C 214 MET cc_start: 0.8667 (mtm) cc_final: 0.8387 (mmm) REVERT: C 229 MET cc_start: 0.5458 (ptp) cc_final: 0.4534 (ptp) REVERT: D 75 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8002 (t80) REVERT: D 159 ASP cc_start: 0.8196 (m-30) cc_final: 0.7853 (m-30) REVERT: D 170 LEU cc_start: 0.9248 (tt) cc_final: 0.8901 (tt) REVERT: D 210 MET cc_start: 0.9033 (ttt) cc_final: 0.8786 (ttt) REVERT: D 238 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8435 (tm-30) REVERT: D 246 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8455 (mp0) REVERT: D 250 GLU cc_start: 0.9399 (tt0) cc_final: 0.9083 (tt0) REVERT: E 55 SER cc_start: 0.8831 (m) cc_final: 0.8347 (p) REVERT: E 152 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8607 (tp30) REVERT: E 204 PHE cc_start: 0.8798 (t80) cc_final: 0.8293 (t80) REVERT: E 210 MET cc_start: 0.8769 (mmt) cc_final: 0.8547 (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: 0.9016 (tp30) REVERT: F 38 GLN cc_start: 0.8243 (tp40) cc_final: 0.7621 (tp40) REVERT: F 45 TRP cc_start: 0.8777 (t60) cc_final: 0.8487 (t60) REVERT: F 62 SER cc_start: 0.8185 (m) cc_final: 0.7739 (t) REVERT: F 139 GLU cc_start: 0.8719 (mp0) cc_final: 0.8489 (mp0) REVERT: F 210 MET cc_start: 0.9056 (mmm) cc_final: 0.8845 (mmm) REVERT: F 263 ILE cc_start: 0.7700 (mt) cc_final: 0.7354 (mm) REVERT: G 124 ASP cc_start: 0.8438 (t0) cc_final: 0.8162 (t0) REVERT: G 213 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7169 (tm-30) REVERT: G 229 MET cc_start: 0.9045 (mpp) cc_final: 0.8749 (pmm) REVERT: H 38 GLN cc_start: 0.8098 (tp40) cc_final: 0.7299 (tp40) REVERT: H 54 LYS cc_start: 0.8765 (tttp) cc_final: 0.8177 (tttp) REVERT: H 103 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8151 (ttmm) REVERT: H 159 ASP cc_start: 0.9238 (t0) cc_final: 0.8948 (t0) REVERT: H 195 ARG cc_start: 0.8145 (tpt170) cc_final: 0.7701 (ptt180) REVERT: H 207 THR cc_start: 0.9513 (m) cc_final: 0.9277 (p) REVERT: H 214 MET cc_start: 0.9223 (mtm) cc_final: 0.8846 (mpp) REVERT: H 246 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8619 (mp0) REVERT: I 38 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: I 140 MET cc_start: 0.7920 (tpp) cc_final: 0.7655 (tpp) REVERT: I 145 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8185 (mp0) REVERT: I 191 ARG cc_start: 0.7877 (mmm160) cc_final: 0.7676 (tpt-90) REVERT: I 199 LEU cc_start: 0.7807 (tp) cc_final: 0.7255 (tp) REVERT: I 214 MET cc_start: 0.8935 (mtt) cc_final: 0.8710 (mtp) REVERT: I 224 LEU cc_start: 0.9302 (mt) cc_final: 0.8972 (mp) REVERT: I 229 MET cc_start: 0.9374 (mpp) cc_final: 0.8952 (pmm) REVERT: I 250 GLU cc_start: 0.9244 (tt0) cc_final: 0.8911 (tt0) REVERT: I 273 LYS cc_start: 0.9422 (mttt) cc_final: 0.8892 (tmtt) REVERT: J 38 GLN cc_start: 0.8685 (tp40) cc_final: 0.8473 (tp40) REVERT: J 93 TYR cc_start: 0.8130 (t80) cc_final: 0.7564 (t80) REVERT: J 104 ASP cc_start: 0.8909 (t70) cc_final: 0.8705 (t0) REVERT: J 116 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7283 (mtm-85) REVERT: J 267 VAL cc_start: 0.8866 (t) cc_final: 0.8337 (t) outliers start: 63 outliers final: 34 residues processed: 459 average time/residue: 0.1329 time to fit residues: 93.6616 Evaluate side-chains 375 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 337 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 245 ASP Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL 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 55 SER Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 196 PHE 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 116 ARG 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 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: 5.9990 chunk 69 optimal weight: 6.9990 chunk 10 optimal weight: 50.0000 chunk 87 optimal weight: 0.0770 chunk 200 optimal weight: 6.9990 chunk 22 optimal weight: 0.0060 chunk 85 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 41 optimal weight: 2.9990 overall best weight: 0.7914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 37 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 77 HIS F 77 HIS F 185 GLN 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.108093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.076532 restraints weight = 61558.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.079128 restraints weight = 31496.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080783 restraints weight = 20502.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.081830 restraints weight = 15581.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.082523 restraints weight = 13100.133| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19279 Z= 0.156 Angle : 0.692 12.832 26167 Z= 0.364 Chirality : 0.045 0.308 2990 Planarity : 0.005 0.046 3205 Dihedral : 14.509 157.657 3021 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.85 % Allowed : 18.47 % Favored : 77.68 % 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: 1.00 (0.14), residues: 1292 sheet: -0.13 (0.52), 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 0.035 0.002 TRP F 20 HIS 0.005 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (19275) covalent geometry : angle 0.69183 / 0.36 (26167) hydrogen bonds : bond 0.05493 / 4.18 ( 903) hydrogen bonds : angle 4.78248 / 3.59 ( 2663) Misc. bond : bond 0.00203 / 0.10 ( 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 453 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 384 time to evaluate : 0.518 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: C 22 GLN cc_start: 0.9200 (mp10) cc_final: 0.8951 (pm20) REVERT: C 29 LYS cc_start: 0.2029 (mmtm) cc_final: 0.1671 (mmtm) REVERT: C 163 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7653 (p0) REVERT: C 183 ASP cc_start: 0.8673 (t0) cc_final: 0.8397 (t0) REVERT: C 214 MET cc_start: 0.8685 (mtm) cc_final: 0.8417 (mmm) REVERT: C 229 MET cc_start: 0.5465 (ptp) cc_final: 0.5151 (pmm) REVERT: D 55 SER cc_start: 0.8848 (m) cc_final: 0.8249 (p) REVERT: D 75 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8111 (t80) REVERT: D 159 ASP cc_start: 0.7980 (m-30) cc_final: 0.7558 (m-30) REVERT: D 170 LEU cc_start: 0.9275 (tt) cc_final: 0.8896 (tt) REVERT: D 187 LEU cc_start: 0.9232 (tp) cc_final: 0.8956 (tp) REVERT: D 204 PHE cc_start: 0.8620 (t80) cc_final: 0.8354 (t80) REVERT: D 207 THR cc_start: 0.9438 (m) cc_final: 0.9215 (p) REVERT: D 210 MET cc_start: 0.8956 (ttt) cc_final: 0.8634 (ttt) REVERT: D 229 MET cc_start: 0.8886 (mpp) cc_final: 0.8267 (pmm) REVERT: D 250 GLU cc_start: 0.9368 (tt0) cc_final: 0.9150 (tt0) REVERT: E 38 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7673 (tp40) REVERT: E 55 SER cc_start: 0.8859 (m) cc_final: 0.8428 (p) REVERT: E 77 HIS cc_start: 0.7795 (m170) cc_final: 0.7576 (m170) REVERT: E 99 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8964 (mmtt) REVERT: E 150 LYS cc_start: 0.8960 (tptp) cc_final: 0.8728 (tptp) REVERT: E 246 GLU cc_start: 0.9347 (tp30) cc_final: 0.8921 (tp30) REVERT: F 45 TRP cc_start: 0.8794 (t60) cc_final: 0.8403 (t60) REVERT: F 55 SER cc_start: 0.9081 (p) cc_final: 0.8704 (p) REVERT: F 62 SER cc_start: 0.8436 (m) cc_final: 0.8205 (t) REVERT: F 127 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8443 (p0) REVERT: F 139 GLU cc_start: 0.8808 (mp0) cc_final: 0.8427 (mp0) REVERT: F 188 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8313 (mm-30) REVERT: F 209 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8835 (pt0) REVERT: F 263 ILE cc_start: 0.7917 (mt) cc_final: 0.7485 (mm) REVERT: F 269 GLN cc_start: 0.8961 (mt0) cc_final: 0.8605 (mt0) REVERT: G 29 LYS cc_start: 0.9217 (pttp) cc_final: 0.8911 (pttm) REVERT: G 124 ASP cc_start: 0.8453 (t0) cc_final: 0.8136 (t0) REVERT: G 159 ASP cc_start: 0.9004 (m-30) cc_final: 0.8707 (m-30) REVERT: G 229 MET cc_start: 0.9052 (mpp) cc_final: 0.8550 (pmm) REVERT: H 28 LEU cc_start: 0.9624 (mm) cc_final: 0.9311 (mp) REVERT: H 38 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7810 (tp40) REVERT: H 73 TYR cc_start: 0.8482 (t80) cc_final: 0.8065 (t80) REVERT: H 159 ASP cc_start: 0.9064 (t0) cc_final: 0.7817 (t0) REVERT: H 162 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7331 (pp20) REVERT: H 163 ASP cc_start: 0.7720 (m-30) cc_final: 0.6922 (m-30) REVERT: H 195 ARG cc_start: 0.8172 (tpt170) cc_final: 0.7675 (ptt180) REVERT: H 214 MET cc_start: 0.9195 (mtm) cc_final: 0.8827 (mpp) REVERT: H 238 GLU cc_start: 0.8026 (mp0) cc_final: 0.7817 (mp0) REVERT: H 246 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8614 (mp0) REVERT: I 38 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8060 (tp40) REVERT: I 97 HIS cc_start: 0.8582 (m-70) cc_final: 0.8229 (m170) REVERT: I 145 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8371 (mm-30) REVERT: I 156 ASP cc_start: 0.9507 (m-30) cc_final: 0.9228 (t0) REVERT: I 199 LEU cc_start: 0.7842 (tp) cc_final: 0.7184 (tp) REVERT: I 210 MET cc_start: 0.9297 (ttt) cc_final: 0.8848 (ttt) REVERT: I 214 MET cc_start: 0.8977 (mtt) cc_final: 0.8741 (mtp) REVERT: I 229 MET cc_start: 0.9326 (mpp) cc_final: 0.8891 (pmm) REVERT: I 246 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8679 (mp0) REVERT: I 273 LYS cc_start: 0.9415 (mttt) cc_final: 0.8898 (tmtt) REVERT: J 38 GLN cc_start: 0.8726 (tp40) cc_final: 0.8403 (tt0) REVERT: J 93 TYR cc_start: 0.8173 (t80) cc_final: 0.7643 (t80) REVERT: J 104 ASP cc_start: 0.9122 (t70) cc_final: 0.8800 (t0) REVERT: J 116 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7236 (mtm-85) outliers start: 69 outliers final: 30 residues processed: 431 average time/residue: 0.1253 time to fit residues: 83.9491 Evaluate side-chains 379 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 341 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 163 ASP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 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 218 LEU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 209 GLU 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 G residue 164 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain H residue 38 GLN 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 208 VAL Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU 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 166 ILE Chi-restraints excluded: chain J residue 196 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 231 optimal weight: 30.0000 chunk 180 optimal weight: 4.9990 chunk 93 optimal weight: 0.0070 chunk 3 optimal weight: 40.0000 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 HIS E 38 GLN F 213 GLN H 38 GLN I 38 GLN I 77 HIS I 185 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3816 r_free = 0.3816 target = 0.105016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.073148 restraints weight = 61694.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.075520 restraints weight = 32712.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077085 restraints weight = 21838.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.078093 restraints weight = 16781.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078712 restraints weight = 14186.286| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19279 Z= 0.208 Angle : 0.696 14.619 26167 Z= 0.369 Chirality : 0.044 0.278 2990 Planarity : 0.004 0.042 3205 Dihedral : 14.451 157.265 3021 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.02 % Allowed : 19.03 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.17), residues: 2338 helix: 1.03 (0.14), residues: 1292 sheet: -0.08 (0.54), residues: 96 loop : 0.26 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 175 TYR 0.022 0.001 TYR F 112 PHE 0.051 0.003 PHE J 154 TRP 0.018 0.002 TRP D 20 HIS 0.009 0.002 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (19275) covalent geometry : angle 0.69579 / 0.37 (26167) hydrogen bonds : bond 0.05308 / 4.05 ( 903) hydrogen bonds : angle 4.89202 / 3.68 ( 2663) Misc. bond : bond 0.00210 / 0.10 ( 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 417 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 345 time to evaluate : 0.745 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: 0.9025 (mtpt) cc_final: 0.8351 (mtpp) REVERT: C 183 ASP cc_start: 0.8616 (t0) cc_final: 0.8383 (t0) REVERT: C 229 MET cc_start: 0.5657 (ptp) cc_final: 0.5321 (pmm) REVERT: D 75 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8171 (t80) REVERT: D 159 ASP cc_start: 0.8136 (m-30) cc_final: 0.7699 (m-30) REVERT: D 170 LEU cc_start: 0.9312 (tt) cc_final: 0.8901 (tt) REVERT: D 196 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8395 (t80) REVERT: D 204 PHE cc_start: 0.8817 (t80) cc_final: 0.8545 (t80) REVERT: D 207 THR cc_start: 0.9486 (m) cc_final: 0.9264 (p) REVERT: D 229 MET cc_start: 0.8844 (mpp) cc_final: 0.8183 (pmm) REVERT: D 250 GLU cc_start: 0.9318 (tt0) cc_final: 0.9068 (tt0) REVERT: E 38 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8048 (tp40) REVERT: E 55 SER cc_start: 0.9020 (m) cc_final: 0.8690 (p) REVERT: E 77 HIS cc_start: 0.7806 (m170) cc_final: 0.7494 (m170) REVERT: E 145 GLU cc_start: 0.7767 (mp0) cc_final: 0.7211 (mp0) REVERT: E 223 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8437 (p0) REVERT: E 229 MET cc_start: 0.8451 (mmm) cc_final: 0.8245 (mmt) REVERT: F 62 SER cc_start: 0.8590 (m) cc_final: 0.8383 (t) REVERT: F 139 GLU cc_start: 0.8854 (mp0) cc_final: 0.8449 (mp0) REVERT: F 144 ASP cc_start: 0.9115 (t0) cc_final: 0.8737 (t0) REVERT: F 145 GLU cc_start: 0.8274 (tt0) cc_final: 0.7315 (tm-30) REVERT: F 185 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8483 (mm-40) REVERT: F 269 GLN cc_start: 0.9069 (mt0) cc_final: 0.8690 (mt0) REVERT: G 29 LYS cc_start: 0.9209 (pttp) cc_final: 0.8995 (pttm) REVERT: G 70 CYS cc_start: 0.9340 (m) cc_final: 0.9138 (m) REVERT: G 124 ASP cc_start: 0.8553 (t0) cc_final: 0.8255 (t0) REVERT: G 159 ASP cc_start: 0.9022 (m-30) cc_final: 0.8752 (m-30) REVERT: G 183 ASP cc_start: 0.8340 (t70) cc_final: 0.8126 (t70) REVERT: G 213 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7310 (tm-30) REVERT: G 214 MET cc_start: 0.8699 (mmm) cc_final: 0.7444 (mmm) REVERT: G 229 MET cc_start: 0.9119 (mpp) cc_final: 0.8877 (pmm) REVERT: H 54 LYS cc_start: 0.8760 (tptp) cc_final: 0.8541 (tttp) REVERT: H 77 HIS cc_start: 0.8602 (m170) cc_final: 0.8054 (m-70) REVERT: H 159 ASP cc_start: 0.9083 (t0) cc_final: 0.7887 (t0) REVERT: H 162 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7312 (pp20) REVERT: H 163 ASP cc_start: 0.7712 (m-30) cc_final: 0.7050 (m-30) REVERT: H 210 MET cc_start: 0.9421 (mpp) cc_final: 0.9090 (mpp) REVERT: H 246 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8721 (mp0) REVERT: I 38 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8021 (tp40) REVERT: I 145 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8447 (mm-30) REVERT: I 199 LEU cc_start: 0.7614 (tp) cc_final: 0.6861 (tp) REVERT: I 210 MET cc_start: 0.9387 (ttt) cc_final: 0.9101 (ttt) REVERT: I 214 MET cc_start: 0.9042 (mtt) cc_final: 0.8837 (mtp) REVERT: I 224 LEU cc_start: 0.9388 (mt) cc_final: 0.8803 (mp) REVERT: I 229 MET cc_start: 0.9314 (mpp) cc_final: 0.8710 (pmm) REVERT: I 246 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8758 (mp0) REVERT: I 273 LYS cc_start: 0.9458 (mttt) cc_final: 0.8941 (tmtt) REVERT: J 38 GLN cc_start: 0.8731 (tp40) cc_final: 0.8222 (tt0) REVERT: J 93 TYR cc_start: 0.8264 (t80) cc_final: 0.7714 (t80) REVERT: J 104 ASP cc_start: 0.9191 (t70) cc_final: 0.8846 (t0) outliers start: 72 outliers final: 45 residues processed: 389 average time/residue: 0.1307 time to fit residues: 80.3689 Evaluate side-chains 365 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 315 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 221 SER 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 109 ILE Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 31 LYS 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 223 ASN Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 168 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 I residue 38 GLN Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 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 216 LEU Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 GLN E 38 GLN F 38 GLN H 38 GLN I 38 GLN I 213 GLN J 97 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.105665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073710 restraints weight = 61427.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076131 restraints weight = 32330.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077708 restraints weight = 21426.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078720 restraints weight = 16388.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079270 restraints weight = 13851.173| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19279 Z= 0.141 Angle : 0.664 11.848 26167 Z= 0.345 Chirality : 0.045 0.328 2990 Planarity : 0.004 0.053 3205 Dihedral : 14.359 156.553 3021 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.12 % Allowed : 21.48 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2338 helix: 1.08 (0.14), residues: 1292 sheet: -0.09 (0.54), residues: 96 loop : 0.27 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 50 TYR 0.017 0.001 TYR F 112 PHE 0.042 0.002 PHE I 125 TRP 0.014 0.002 TRP H 45 HIS 0.004 0.001 HIS I 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (19275) covalent geometry : angle 0.66413 / 0.34 (26167) hydrogen bonds : bond 0.04792 / 3.66 ( 903) hydrogen bonds : angle 4.72396 / 3.55 ( 2663) Misc. bond : bond 0.00145 / 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 406 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 350 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 GLN cc_start: 0.8828 (mp10) cc_final: 0.8386 (pm20) REVERT: C 29 LYS cc_start: 0.3070 (mmtt) cc_final: 0.2676 (mmtp) REVERT: C 107 LYS cc_start: 0.9347 (tttm) cc_final: 0.8602 (tptm) REVERT: C 111 GLU cc_start: 0.8608 (mt-10) cc_final: 0.6930 (mt-10) REVERT: C 183 ASP cc_start: 0.8611 (t0) cc_final: 0.8343 (t0) REVERT: C 229 MET cc_start: 0.5575 (ptp) cc_final: 0.5207 (pmm) REVERT: D 54 LYS cc_start: 0.9106 (mmpt) cc_final: 0.8780 (mmtt) REVERT: D 75 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8108 (t80) REVERT: D 159 ASP cc_start: 0.8178 (m-30) cc_final: 0.7704 (m-30) REVERT: D 170 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8853 (tt) REVERT: D 196 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8330 (t80) REVERT: D 204 PHE cc_start: 0.8830 (t80) cc_final: 0.8533 (t80) REVERT: D 207 THR cc_start: 0.9513 (m) cc_final: 0.9311 (p) REVERT: D 210 MET cc_start: 0.9282 (mtp) cc_final: 0.8721 (ttt) REVERT: D 229 MET cc_start: 0.8885 (mpp) cc_final: 0.8192 (pmm) REVERT: E 38 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7979 (tp40) REVERT: E 55 SER cc_start: 0.9057 (m) cc_final: 0.8680 (p) REVERT: E 77 HIS cc_start: 0.7839 (m170) cc_final: 0.7474 (m-70) REVERT: E 145 GLU cc_start: 0.7764 (mp0) cc_final: 0.7206 (mp0) REVERT: E 150 LYS cc_start: 0.9043 (tptp) cc_final: 0.8820 (tptp) REVERT: E 163 ASP cc_start: 0.7363 (p0) cc_final: 0.6887 (p0) REVERT: E 179 VAL cc_start: 0.9010 (t) cc_final: 0.8655 (p) REVERT: E 210 MET cc_start: 0.8987 (mmm) cc_final: 0.8550 (mpp) REVERT: E 229 MET cc_start: 0.8295 (mmm) cc_final: 0.8083 (mmm) REVERT: F 139 GLU cc_start: 0.8831 (mp0) cc_final: 0.8446 (mp0) REVERT: F 144 ASP cc_start: 0.9067 (t0) cc_final: 0.8674 (t0) REVERT: F 145 GLU cc_start: 0.8286 (tt0) cc_final: 0.7292 (tm-30) REVERT: F 185 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8353 (mm-40) REVERT: F 188 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8463 (mm-30) REVERT: F 229 MET cc_start: 0.8955 (pmm) cc_final: 0.8503 (pmm) REVERT: G 70 CYS cc_start: 0.9333 (m) cc_final: 0.9119 (m) REVERT: G 124 ASP cc_start: 0.8490 (t0) cc_final: 0.8150 (t0) REVERT: G 159 ASP cc_start: 0.8929 (m-30) cc_final: 0.8609 (m-30) REVERT: G 183 ASP cc_start: 0.8282 (t70) cc_final: 0.8076 (t70) REVERT: G 213 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7496 (pp30) REVERT: G 214 MET cc_start: 0.8562 (mmm) cc_final: 0.8328 (mmp) REVERT: G 229 MET cc_start: 0.9183 (mpp) cc_final: 0.8690 (pmm) REVERT: H 54 LYS cc_start: 0.8704 (tptp) cc_final: 0.8458 (tptt) REVERT: H 140 MET cc_start: 0.8241 (ttm) cc_final: 0.8031 (ttm) REVERT: H 159 ASP cc_start: 0.9103 (t0) cc_final: 0.7900 (t0) REVERT: H 162 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7264 (pp20) REVERT: H 163 ASP cc_start: 0.7697 (m-30) cc_final: 0.7002 (m-30) REVERT: H 210 MET cc_start: 0.9411 (mpp) cc_final: 0.8970 (mpp) REVERT: H 214 MET cc_start: 0.9222 (mtm) cc_final: 0.8827 (mpp) REVERT: H 246 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8684 (mp0) REVERT: I 38 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8341 (tp40) REVERT: I 97 HIS cc_start: 0.8494 (m-70) cc_final: 0.8221 (m170) REVERT: I 107 LYS cc_start: 0.9422 (ptmm) cc_final: 0.9220 (pptt) REVERT: I 145 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8395 (mm-30) REVERT: I 156 ASP cc_start: 0.9535 (OUTLIER) cc_final: 0.9290 (t0) REVERT: I 160 ILE cc_start: 0.9404 (mp) cc_final: 0.9157 (mp) REVERT: I 199 LEU cc_start: 0.7688 (tp) cc_final: 0.7184 (tp) REVERT: I 210 MET cc_start: 0.9435 (ttt) cc_final: 0.9184 (ttt) REVERT: I 214 MET cc_start: 0.9010 (mtt) cc_final: 0.8805 (mtp) REVERT: I 229 MET cc_start: 0.9330 (mpp) cc_final: 0.8618 (pmm) REVERT: I 246 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8802 (mp0) REVERT: I 273 LYS cc_start: 0.9443 (mttt) cc_final: 0.8914 (tmtt) REVERT: J 38 GLN cc_start: 0.8717 (tp40) cc_final: 0.8253 (tt0) REVERT: J 104 ASP cc_start: 0.9208 (t70) cc_final: 0.8853 (t0) REVERT: J 246 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8820 (mm-30) outliers start: 56 outliers final: 33 residues processed: 386 average time/residue: 0.1326 time to fit residues: 80.5300 Evaluate side-chains 356 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 317 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 D residue 33 ILE Chi-restraints excluded: chain D residue 38 GLN 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 196 PHE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 246 GLU 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 218 LEU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 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 91 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 233 LEU 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 34 VAL Chi-restraints excluded: chain J residue 53 ARG 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: 0.9990 chunk 190 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 206 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 37 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 HIS I 38 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.105726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.074110 restraints weight = 61566.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.076569 restraints weight = 32015.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.078146 restraints weight = 21003.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.079141 restraints weight = 16032.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.079810 restraints weight = 13515.191| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19279 Z= 0.142 Angle : 0.659 12.393 26167 Z= 0.342 Chirality : 0.044 0.227 2990 Planarity : 0.004 0.039 3205 Dihedral : 14.290 156.390 3021 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.85 % Allowed : 21.21 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2338 helix: 1.09 (0.14), residues: 1292 sheet: -0.12 (0.54), residues: 96 loop : 0.24 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 85 TYR 0.016 0.001 TYR F 112 PHE 0.040 0.002 PHE I 125 TRP 0.026 0.002 TRP D 20 HIS 0.003 0.001 HIS J 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (19275) covalent geometry : angle 0.65889 / 0.34 (26167) hydrogen bonds : bond 0.04561 / 3.49 ( 903) hydrogen bonds : angle 4.69205 / 3.52 ( 2663) Misc. bond : bond 0.00150 / 0.08 ( 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 400 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 331 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 GLN cc_start: 0.8783 (mp10) cc_final: 0.8351 (pm20) REVERT: C 29 LYS cc_start: 0.2738 (mmtt) cc_final: 0.2533 (mmtm) REVERT: C 54 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8372 (mtpp) REVERT: C 183 ASP cc_start: 0.8653 (t0) cc_final: 0.8395 (t0) REVERT: C 229 MET cc_start: 0.5696 (ptp) cc_final: 0.5340 (pmm) REVERT: D 75 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.8117 (t80) REVERT: D 159 ASP cc_start: 0.8204 (m-30) cc_final: 0.7711 (m-30) REVERT: D 170 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8855 (tt) REVERT: D 204 PHE cc_start: 0.8791 (t80) cc_final: 0.8479 (t80) REVERT: D 210 MET cc_start: 0.9264 (mtp) cc_final: 0.8698 (ttt) REVERT: D 229 MET cc_start: 0.9030 (mpp) cc_final: 0.8213 (pmm) REVERT: D 250 GLU cc_start: 0.9170 (tt0) cc_final: 0.8887 (tt0) REVERT: E 55 SER cc_start: 0.9075 (m) cc_final: 0.8732 (p) REVERT: E 145 GLU cc_start: 0.7782 (mp0) cc_final: 0.7233 (mp0) REVERT: E 163 ASP cc_start: 0.7220 (p0) cc_final: 0.6720 (p0) REVERT: E 179 VAL cc_start: 0.9002 (t) cc_final: 0.8655 (p) REVERT: E 229 MET cc_start: 0.8314 (mmm) cc_final: 0.8087 (mmm) REVERT: F 134 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8615 (mtmm) REVERT: F 139 GLU cc_start: 0.8824 (mp0) cc_final: 0.8436 (mp0) REVERT: F 144 ASP cc_start: 0.9058 (t0) cc_final: 0.8640 (t0) REVERT: F 145 GLU cc_start: 0.8268 (tt0) cc_final: 0.7312 (tm-30) REVERT: F 185 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8308 (mm-40) REVERT: F 188 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8479 (mm-30) REVERT: G 124 ASP cc_start: 0.8485 (t0) cc_final: 0.8146 (t0) REVERT: G 159 ASP cc_start: 0.8763 (m-30) cc_final: 0.8406 (m-30) REVERT: G 184 GLU cc_start: 0.8640 (mp0) cc_final: 0.8348 (mp0) REVERT: G 229 MET cc_start: 0.9187 (mpp) cc_final: 0.8642 (pmm) REVERT: H 54 LYS cc_start: 0.8736 (tptp) cc_final: 0.8457 (tptt) REVERT: H 159 ASP cc_start: 0.9146 (t0) cc_final: 0.8534 (t0) REVERT: H 163 ASP cc_start: 0.7733 (m-30) cc_final: 0.7428 (m-30) REVERT: H 210 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.8963 (mpp) REVERT: H 214 MET cc_start: 0.9232 (mtm) cc_final: 0.8811 (mpp) REVERT: H 246 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8676 (mp0) REVERT: I 38 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: I 97 HIS cc_start: 0.8588 (m-70) cc_final: 0.8155 (m170) REVERT: I 107 LYS cc_start: 0.9427 (ptmm) cc_final: 0.9207 (pptt) REVERT: I 145 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8427 (mm-30) REVERT: I 156 ASP cc_start: 0.9486 (OUTLIER) cc_final: 0.9214 (t0) REVERT: I 160 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9106 (mp) REVERT: I 199 LEU cc_start: 0.7802 (tp) cc_final: 0.7146 (tp) REVERT: I 210 MET cc_start: 0.9342 (ttt) cc_final: 0.9096 (ttt) REVERT: I 214 MET cc_start: 0.9021 (mtt) cc_final: 0.8810 (mtp) REVERT: I 229 MET cc_start: 0.9291 (mpp) cc_final: 0.8767 (pmm) REVERT: I 246 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8816 (mp0) REVERT: I 273 LYS cc_start: 0.9475 (mttt) cc_final: 0.8930 (tmtt) REVERT: J 38 GLN cc_start: 0.8658 (tp40) cc_final: 0.8208 (tt0) REVERT: J 104 ASP cc_start: 0.9225 (t70) cc_final: 0.8857 (t0) REVERT: J 229 MET cc_start: 0.9082 (ptp) cc_final: 0.8527 (ppp) REVERT: J 246 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8873 (mm-30) outliers start: 69 outliers final: 48 residues processed: 373 average time/residue: 0.1300 time to fit residues: 76.7129 Evaluate side-chains 365 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 232 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 156 ASP 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 H residue 91 VAL 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 210 MET Chi-restraints excluded: chain H residue 233 LEU 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 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 Chi-restraints excluded: chain J residue 216 LEU 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: 10.0000 chunk 213 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 77 HIS I 213 GLN J 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.103864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072566 restraints weight = 62512.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.074930 restraints weight = 32956.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.076465 restraints weight = 21889.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.077465 restraints weight = 16842.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.078036 restraints weight = 14246.632| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19279 Z= 0.183 Angle : 0.671 11.962 26167 Z= 0.351 Chirality : 0.044 0.257 2990 Planarity : 0.004 0.044 3205 Dihedral : 14.223 156.486 3021 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.30 % Allowed : 21.32 % 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: 1.11 (0.15), residues: 1292 sheet: -0.08 (0.40), residues: 192 loop : 0.31 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 231 TYR 0.021 0.001 TYR F 112 PHE 0.045 0.003 PHE I 125 TRP 0.013 0.001 TRP H 45 HIS 0.004 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (19275) covalent geometry : angle 0.67084 / 0.35 (26167) hydrogen bonds : bond 0.04697 / 3.60 ( 903) hydrogen bonds : angle 4.77107 / 3.58 ( 2663) Misc. bond : bond 0.00183 / 0.09 ( 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 400 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 323 time to evaluate : 0.772 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: 0.8897 (mp10) cc_final: 0.8488 (pm20) REVERT: C 29 LYS cc_start: 0.3060 (mmtt) cc_final: 0.2831 (mmtm) REVERT: C 54 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8426 (mtpp) REVERT: C 183 ASP cc_start: 0.8627 (t0) cc_final: 0.8345 (t0) REVERT: C 229 MET cc_start: 0.6087 (ptp) cc_final: 0.5642 (pmm) REVERT: D 38 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8446 (mp10) REVERT: D 75 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8161 (t80) REVERT: D 99 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8740 (mmtm) REVERT: D 159 ASP cc_start: 0.8297 (m-30) cc_final: 0.7795 (m-30) REVERT: D 210 MET cc_start: 0.9247 (mtp) cc_final: 0.8693 (ttt) REVERT: D 229 MET cc_start: 0.9036 (mpp) cc_final: 0.8746 (mpp) REVERT: D 250 GLU cc_start: 0.9130 (tt0) cc_final: 0.8878 (tt0) REVERT: E 55 SER cc_start: 0.9110 (m) cc_final: 0.8818 (p) REVERT: E 77 HIS cc_start: 0.7805 (m170) cc_final: 0.7457 (m-70) REVERT: E 145 GLU cc_start: 0.7845 (mp0) cc_final: 0.7327 (mp0) REVERT: E 210 MET cc_start: 0.9007 (mmm) cc_final: 0.8603 (mpp) REVERT: E 229 MET cc_start: 0.8325 (mmm) cc_final: 0.8101 (mmm) REVERT: F 134 LYS cc_start: 0.8945 (mtmm) cc_final: 0.8667 (mtmm) REVERT: F 139 GLU cc_start: 0.8732 (mp0) cc_final: 0.8427 (mp0) REVERT: F 144 ASP cc_start: 0.8997 (t0) cc_final: 0.8689 (t0) REVERT: F 145 GLU cc_start: 0.8474 (tt0) cc_final: 0.7442 (tm-30) REVERT: F 185 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8225 (mm-40) REVERT: F 188 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8524 (mm-30) REVERT: G 124 ASP cc_start: 0.8517 (t0) cc_final: 0.8162 (t0) REVERT: G 159 ASP cc_start: 0.8678 (m-30) cc_final: 0.8367 (m-30) REVERT: G 229 MET cc_start: 0.9187 (mpp) cc_final: 0.8598 (pmm) REVERT: G 268 LEU cc_start: 0.9394 (mt) cc_final: 0.9156 (tp) REVERT: H 54 LYS cc_start: 0.8765 (tptp) cc_final: 0.8398 (tptt) REVERT: H 159 ASP cc_start: 0.9142 (t0) cc_final: 0.8539 (t0) REVERT: H 163 ASP cc_start: 0.7833 (m-30) cc_final: 0.7528 (m-30) REVERT: H 214 MET cc_start: 0.9221 (mtm) cc_final: 0.8996 (mtm) REVERT: H 246 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8674 (mp0) REVERT: I 38 GLN cc_start: 0.8898 (tp40) cc_final: 0.8421 (tp40) REVERT: I 70 CYS cc_start: 0.8890 (m) cc_final: 0.8659 (p) REVERT: I 97 HIS cc_start: 0.8614 (m-70) cc_final: 0.8159 (m170) REVERT: I 107 LYS cc_start: 0.9422 (ptmm) cc_final: 0.9199 (pptt) REVERT: I 140 MET cc_start: 0.8176 (tpp) cc_final: 0.7638 (tpp) REVERT: I 145 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8492 (mm-30) REVERT: I 156 ASP cc_start: 0.9397 (OUTLIER) cc_final: 0.9164 (t0) REVERT: I 160 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9060 (mp) REVERT: I 199 LEU cc_start: 0.7735 (tp) cc_final: 0.7004 (tp) REVERT: I 229 MET cc_start: 0.9307 (mpp) cc_final: 0.8869 (pmm) REVERT: I 246 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8852 (mp0) REVERT: I 273 LYS cc_start: 0.9501 (mttt) cc_final: 0.8944 (tmtt) REVERT: J 38 GLN cc_start: 0.8703 (tp40) cc_final: 0.8456 (tt0) REVERT: J 104 ASP cc_start: 0.9284 (t70) cc_final: 0.8925 (t0) REVERT: J 224 LEU cc_start: 0.9164 (mt) cc_final: 0.8941 (mt) REVERT: J 229 MET cc_start: 0.9100 (ptp) cc_final: 0.8564 (ppp) REVERT: J 246 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8939 (mm-30) outliers start: 77 outliers final: 56 residues processed: 367 average time/residue: 0.1287 time to fit residues: 74.8937 Evaluate side-chains 363 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 303 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 SER 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 221 SER Chi-restraints excluded: chain C residue 232 ILE 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 109 ILE 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 199 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 247 ILE 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 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 138 VAL 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 268 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 253 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 131 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 212 optimal weight: 0.0010 chunk 92 optimal weight: 0.8980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN J 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.104638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.073049 restraints weight = 62896.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075336 restraints weight = 33868.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076857 restraints weight = 22868.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077776 restraints weight = 17777.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.078400 restraints weight = 15198.961| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19279 Z= 0.135 Angle : 0.692 13.454 26167 Z= 0.353 Chirality : 0.044 0.245 2990 Planarity : 0.004 0.042 3205 Dihedral : 14.168 156.306 3021 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.57 % Allowed : 22.21 % Favored : 74.22 % 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: 0.89 (0.17), residues: 2338 helix: 1.03 (0.15), residues: 1300 sheet: -0.06 (0.40), residues: 192 loop : 0.26 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 189 TYR 0.020 0.001 TYR J 75 PHE 0.045 0.002 PHE I 125 TRP 0.016 0.001 TRP J 211 HIS 0.009 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (19275) covalent geometry : angle 0.69194 / 0.35 (26167) hydrogen bonds : bond 0.04463 / 3.41 ( 903) hydrogen bonds : angle 4.70410 / 3.53 ( 2663) Misc. bond : bond 0.00133 / 0.07 ( 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 382 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 318 time to evaluate : 0.764 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: 0.3229 (mmtt) cc_final: 0.2747 (mmtp) REVERT: C 54 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8406 (mtpp) REVERT: C 131 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8477 (tm-30) REVERT: C 183 ASP cc_start: 0.8615 (t0) cc_final: 0.8354 (t0) REVERT: C 210 MET cc_start: 0.8713 (ptm) cc_final: 0.8500 (ptp) REVERT: C 229 MET cc_start: 0.6106 (ptp) cc_final: 0.5657 (pmm) REVERT: D 75 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.8142 (t80) REVERT: D 99 LYS cc_start: 0.8987 (mmtp) cc_final: 0.8662 (mmtp) REVERT: D 159 ASP cc_start: 0.8270 (m-30) cc_final: 0.7762 (m-30) REVERT: D 210 MET cc_start: 0.9231 (mtp) cc_final: 0.8676 (ttt) REVERT: D 229 MET cc_start: 0.9050 (mpp) cc_final: 0.8002 (ptp) REVERT: D 250 GLU cc_start: 0.9150 (tt0) cc_final: 0.8896 (tt0) REVERT: E 55 SER cc_start: 0.9103 (m) cc_final: 0.8802 (p) REVERT: E 77 HIS cc_start: 0.7935 (m170) cc_final: 0.7555 (m-70) REVERT: E 145 GLU cc_start: 0.7808 (mp0) cc_final: 0.7282 (mp0) REVERT: E 179 VAL cc_start: 0.9053 (t) cc_final: 0.8694 (p) REVERT: E 210 MET cc_start: 0.8965 (mmm) cc_final: 0.8650 (mpp) REVERT: E 229 MET cc_start: 0.8350 (mmm) cc_final: 0.8123 (mmm) REVERT: F 125 PHE cc_start: 0.9263 (m-80) cc_final: 0.8957 (m-80) REVERT: F 134 LYS cc_start: 0.8969 (mtmm) cc_final: 0.8700 (mtmm) REVERT: F 139 GLU cc_start: 0.8687 (mp0) cc_final: 0.8376 (mp0) REVERT: F 144 ASP cc_start: 0.8960 (t0) cc_final: 0.8623 (t0) REVERT: F 145 GLU cc_start: 0.8473 (tt0) cc_final: 0.7398 (tm-30) REVERT: F 185 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8144 (mm-40) REVERT: F 229 MET cc_start: 0.8942 (pmm) cc_final: 0.8440 (pmm) REVERT: G 124 ASP cc_start: 0.8512 (t0) cc_final: 0.8174 (t0) REVERT: G 159 ASP cc_start: 0.8659 (m-30) cc_final: 0.8310 (m-30) REVERT: G 229 MET cc_start: 0.9193 (mpp) cc_final: 0.8770 (pmm) REVERT: G 268 LEU cc_start: 0.9437 (mt) cc_final: 0.9210 (tp) REVERT: H 54 LYS cc_start: 0.8751 (tptp) cc_final: 0.8266 (tptt) REVERT: H 159 ASP cc_start: 0.9112 (t0) cc_final: 0.8532 (t0) REVERT: H 163 ASP cc_start: 0.7767 (m-30) cc_final: 0.7453 (m-30) REVERT: H 214 MET cc_start: 0.9247 (mtm) cc_final: 0.8788 (mpp) REVERT: H 246 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8683 (mp0) REVERT: H 256 LEU cc_start: 0.9201 (tt) cc_final: 0.8984 (tt) REVERT: I 38 GLN cc_start: 0.8709 (tp40) cc_final: 0.8424 (tp40) REVERT: I 70 CYS cc_start: 0.8885 (m) cc_final: 0.8642 (p) REVERT: I 97 HIS cc_start: 0.8636 (m-70) cc_final: 0.8164 (m170) REVERT: I 107 LYS cc_start: 0.9424 (ptmm) cc_final: 0.9184 (pptt) REVERT: I 145 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8471 (mm-30) REVERT: I 156 ASP cc_start: 0.9395 (OUTLIER) cc_final: 0.9167 (t0) REVERT: I 160 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.8997 (mp) REVERT: I 199 LEU cc_start: 0.7792 (tp) cc_final: 0.7002 (tp) REVERT: I 210 MET cc_start: 0.9319 (ttt) cc_final: 0.9035 (ttt) REVERT: I 214 MET cc_start: 0.9020 (mtp) cc_final: 0.8743 (mtp) REVERT: I 229 MET cc_start: 0.9329 (mpp) cc_final: 0.8880 (pmm) REVERT: I 246 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8793 (tm-30) REVERT: I 273 LYS cc_start: 0.9490 (mttt) cc_final: 0.8927 (tmtt) REVERT: J 38 GLN cc_start: 0.8740 (tp40) cc_final: 0.8453 (tt0) REVERT: J 104 ASP cc_start: 0.9346 (t70) cc_final: 0.9005 (t0) REVERT: J 229 MET cc_start: 0.9106 (ptp) cc_final: 0.8552 (ppp) REVERT: J 246 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8908 (mm-30) outliers start: 64 outliers final: 50 residues processed: 356 average time/residue: 0.1324 time to fit residues: 74.6777 Evaluate side-chains 355 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 302 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 SER 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 196 PHE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 33 ILE 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 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 247 ILE 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 218 LEU Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 91 VAL 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 248 LEU Chi-restraints excluded: chain H residue 253 ILE 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 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 216 LEU 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: 0.0470 chunk 146 optimal weight: 2.9990 chunk 86 optimal weight: 0.0270 chunk 85 optimal weight: 0.0970 chunk 180 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.8336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS J 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.104793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073125 restraints weight = 62488.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075421 restraints weight = 33812.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076913 restraints weight = 22900.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077825 restraints weight = 17862.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078442 restraints weight = 15335.393| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.6403 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= 0.133 Angle : 0.711 13.286 26167 Z= 0.357 Chirality : 0.044 0.249 2990 Planarity : 0.004 0.042 3205 Dihedral : 14.111 156.381 3021 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.24 % Allowed : 23.27 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2338 helix: 1.06 (0.15), residues: 1300 sheet: -0.08 (0.40), residues: 192 loop : 0.23 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG D 231 TYR 0.016 0.001 TYR F 112 PHE 0.045 0.002 PHE I 125 TRP 0.020 0.001 TRP J 211 HIS 0.008 0.001 HIS J 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (19275) covalent geometry : angle 0.71127 / 0.36 (26167) hydrogen bonds : bond 0.04272 / 3.26 ( 903) hydrogen bonds : angle 4.66206 / 3.51 ( 2663) Misc. bond : bond 0.00131 / 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: 58 poor density : 313 time to evaluate : 0.654 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: 0.3137 (mmtt) cc_final: 0.2875 (mmtm) REVERT: C 54 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8252 (mtpp) REVERT: C 183 ASP cc_start: 0.8536 (t0) cc_final: 0.8250 (t0) REVERT: C 210 MET cc_start: 0.8721 (ptm) cc_final: 0.8511 (ptp) REVERT: C 229 MET cc_start: 0.6121 (ptp) cc_final: 0.5666 (pmm) REVERT: D 38 GLN cc_start: 0.9085 (mp10) cc_final: 0.8692 (tt0) REVERT: D 75 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8168 (t80) REVERT: D 140 MET cc_start: 0.8074 (mtp) cc_final: 0.7857 (ttm) REVERT: D 145 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8431 (mm-30) REVERT: D 159 ASP cc_start: 0.8226 (m-30) cc_final: 0.7704 (m-30) REVERT: D 204 PHE cc_start: 0.8949 (t80) cc_final: 0.8746 (t80) REVERT: D 210 MET cc_start: 0.9219 (mtp) cc_final: 0.8666 (ttt) REVERT: D 229 MET cc_start: 0.8842 (mpp) cc_final: 0.7857 (ptp) REVERT: D 250 GLU cc_start: 0.9150 (tt0) cc_final: 0.8910 (tt0) REVERT: D 275 TYR cc_start: 0.7559 (m-80) cc_final: 0.6376 (m-80) REVERT: E 55 SER cc_start: 0.9096 (m) cc_final: 0.8798 (p) REVERT: E 77 HIS cc_start: 0.7927 (m170) cc_final: 0.7569 (m-70) REVERT: E 145 GLU cc_start: 0.7841 (mp0) cc_final: 0.7335 (mp0) REVERT: E 179 VAL cc_start: 0.9034 (t) cc_final: 0.8689 (p) REVERT: E 185 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7453 (tp-100) REVERT: E 229 MET cc_start: 0.8334 (mmm) cc_final: 0.8104 (mmm) REVERT: F 125 PHE cc_start: 0.9250 (m-80) cc_final: 0.8939 (m-80) REVERT: F 139 GLU cc_start: 0.8663 (mp0) cc_final: 0.8366 (mp0) REVERT: F 145 GLU cc_start: 0.8464 (tt0) cc_final: 0.7373 (tm-30) REVERT: F 185 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8116 (mm-40) REVERT: F 214 MET cc_start: 0.9208 (mmm) cc_final: 0.8932 (mmp) REVERT: F 229 MET cc_start: 0.8964 (pmm) cc_final: 0.8491 (pmm) REVERT: G 124 ASP cc_start: 0.8509 (t0) cc_final: 0.8171 (t0) REVERT: G 159 ASP cc_start: 0.8625 (m-30) cc_final: 0.8286 (m-30) REVERT: G 229 MET cc_start: 0.9183 (mpp) cc_final: 0.8761 (pmm) REVERT: G 268 LEU cc_start: 0.9432 (mt) cc_final: 0.9227 (tp) REVERT: H 54 LYS cc_start: 0.8760 (tptp) cc_final: 0.8283 (tptt) REVERT: H 104 ASP cc_start: 0.8567 (t0) cc_final: 0.8066 (t0) REVERT: H 159 ASP cc_start: 0.9099 (t0) cc_final: 0.8557 (t0) REVERT: H 163 ASP cc_start: 0.7761 (m-30) cc_final: 0.7459 (m-30) REVERT: H 214 MET cc_start: 0.9209 (mtm) cc_final: 0.8780 (mpp) REVERT: H 246 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8649 (mp0) REVERT: I 38 GLN cc_start: 0.8705 (tp40) cc_final: 0.8288 (tp40) REVERT: I 70 CYS cc_start: 0.8907 (m) cc_final: 0.8664 (p) REVERT: I 97 HIS cc_start: 0.8651 (m-70) cc_final: 0.8198 (m170) REVERT: I 107 LYS cc_start: 0.9415 (ptmm) cc_final: 0.9168 (pptt) REVERT: I 140 MET cc_start: 0.8039 (tpp) cc_final: 0.7645 (tpp) REVERT: I 145 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8484 (mm-30) REVERT: I 156 ASP cc_start: 0.9368 (OUTLIER) cc_final: 0.9147 (t0) REVERT: I 160 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8889 (mp) REVERT: I 199 LEU cc_start: 0.7965 (tp) cc_final: 0.7404 (tp) REVERT: I 210 MET cc_start: 0.9327 (ttt) cc_final: 0.9051 (ttt) REVERT: I 214 MET cc_start: 0.9020 (mtp) cc_final: 0.8729 (mtp) REVERT: I 229 MET cc_start: 0.9300 (mpp) cc_final: 0.8820 (pmm) REVERT: I 246 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8798 (tm-30) REVERT: I 273 LYS cc_start: 0.9498 (mttt) cc_final: 0.8946 (tmtt) REVERT: J 38 GLN cc_start: 0.8724 (tp40) cc_final: 0.8195 (tt0) REVERT: J 104 ASP cc_start: 0.9347 (t70) cc_final: 0.9055 (t0) REVERT: J 229 MET cc_start: 0.9111 (ptp) cc_final: 0.8491 (ppp) REVERT: J 230 LEU cc_start: 0.9835 (tt) cc_final: 0.9604 (mt) REVERT: J 246 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8922 (mm-30) outliers start: 58 outliers final: 42 residues processed: 347 average time/residue: 0.1291 time to fit residues: 71.1981 Evaluate side-chains 350 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 245 ASP 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 199 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain H residue 91 VAL 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 248 LEU Chi-restraints excluded: chain H residue 253 ILE 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 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: 0.8980 chunk 153 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 88 optimal weight: 0.0670 chunk 2 optimal weight: 20.0000 chunk 52 optimal weight: 0.0050 chunk 138 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.105127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073371 restraints weight = 63084.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075661 restraints weight = 34360.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.077183 restraints weight = 23327.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.078043 restraints weight = 18199.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.078702 restraints weight = 15692.830| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 0.053 19279 Z= 0.127 Angle : 0.706 12.976 26167 Z= 0.354 Chirality : 0.044 0.275 2990 Planarity : 0.004 0.042 3205 Dihedral : 14.026 156.325 3021 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.73 % Allowed : 23.55 % Favored : 73.72 % 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: 0.89 (0.17), residues: 2338 helix: 1.07 (0.15), residues: 1300 sheet: -0.35 (0.53), residues: 96 loop : 0.18 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 231 TYR 0.023 0.001 TYR J 75 PHE 0.045 0.002 PHE I 125 TRP 0.019 0.001 TRP J 211 HIS 0.005 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (19275) covalent geometry : angle 0.70583 / 0.35 (26167) hydrogen bonds : bond 0.04030 / 3.08 ( 903) hydrogen bonds : angle 4.60748 / 3.46 ( 2663) Misc. bond : bond 0.00105 / 0.05 ( 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 374 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 325 time to evaluate : 0.759 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 29 LYS cc_start: 0.3028 (mmtt) cc_final: 0.2712 (mmtm) REVERT: C 131 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8461 (tm-30) REVERT: C 140 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7522 (mpp) REVERT: C 183 ASP cc_start: 0.8487 (t0) cc_final: 0.8213 (t0) REVERT: C 210 MET cc_start: 0.8662 (ptm) cc_final: 0.8456 (ptp) REVERT: C 229 MET cc_start: 0.6140 (ptp) cc_final: 0.5679 (pmm) REVERT: D 75 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8234 (t80) REVERT: D 99 LYS cc_start: 0.9262 (mmmm) cc_final: 0.8875 (mmtp) REVERT: D 145 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8213 (mm-30) REVERT: D 159 ASP cc_start: 0.8255 (m-30) cc_final: 0.7724 (m-30) REVERT: D 180 ILE cc_start: 0.9060 (tt) cc_final: 0.8812 (tt) REVERT: D 187 LEU cc_start: 0.9460 (tt) cc_final: 0.8931 (mt) REVERT: D 204 PHE cc_start: 0.8947 (t80) cc_final: 0.8716 (t80) REVERT: D 210 MET cc_start: 0.9201 (mtp) cc_final: 0.8655 (ttt) REVERT: D 229 MET cc_start: 0.8959 (mpp) cc_final: 0.8631 (mpp) REVERT: E 55 SER cc_start: 0.9085 (m) cc_final: 0.8763 (p) REVERT: E 77 HIS cc_start: 0.7917 (m170) cc_final: 0.7561 (m-70) REVERT: E 145 GLU cc_start: 0.7841 (mp0) cc_final: 0.7349 (mp0) REVERT: E 179 VAL cc_start: 0.8962 (t) cc_final: 0.8621 (p) REVERT: E 185 GLN cc_start: 0.7828 (tp-100) cc_final: 0.7296 (tp-100) REVERT: E 229 MET cc_start: 0.8323 (mmm) cc_final: 0.8101 (mmm) REVERT: E 238 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8433 (mp0) REVERT: F 125 PHE cc_start: 0.9231 (m-80) cc_final: 0.8898 (m-80) REVERT: F 139 GLU cc_start: 0.8640 (mp0) cc_final: 0.8383 (mp0) REVERT: F 145 GLU cc_start: 0.8488 (tt0) cc_final: 0.7348 (tm-30) REVERT: F 185 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8089 (mm-40) REVERT: F 214 MET cc_start: 0.9218 (mmm) cc_final: 0.8931 (mmp) REVERT: F 229 MET cc_start: 0.8975 (pmm) cc_final: 0.8512 (pmm) REVERT: G 124 ASP cc_start: 0.8479 (t0) cc_final: 0.8127 (t0) REVERT: G 159 ASP cc_start: 0.8718 (m-30) cc_final: 0.8307 (m-30) REVERT: G 210 MET cc_start: 0.9042 (ttt) cc_final: 0.8359 (tpp) REVERT: G 229 MET cc_start: 0.9179 (mpp) cc_final: 0.8765 (pmm) REVERT: H 54 LYS cc_start: 0.8803 (tptp) cc_final: 0.8429 (tptt) REVERT: H 159 ASP cc_start: 0.9076 (t0) cc_final: 0.8485 (t0) REVERT: H 163 ASP cc_start: 0.7756 (m-30) cc_final: 0.7448 (m-30) REVERT: H 214 MET cc_start: 0.9174 (mtm) cc_final: 0.8736 (mpp) REVERT: H 246 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8638 (mp0) REVERT: I 38 GLN cc_start: 0.8653 (tp40) cc_final: 0.8247 (tp40) REVERT: I 97 HIS cc_start: 0.8664 (m-70) cc_final: 0.8196 (m170) REVERT: I 107 LYS cc_start: 0.9431 (ptmm) cc_final: 0.9166 (pptt) REVERT: I 145 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8499 (mm-30) REVERT: I 150 LYS cc_start: 0.8265 (mttt) cc_final: 0.7841 (mtpt) REVERT: I 199 LEU cc_start: 0.7966 (tp) cc_final: 0.7413 (tp) REVERT: I 210 MET cc_start: 0.9388 (ttt) cc_final: 0.9111 (ttt) REVERT: I 214 MET cc_start: 0.9009 (mtp) cc_final: 0.8768 (mtp) REVERT: I 229 MET cc_start: 0.9308 (mpp) cc_final: 0.8851 (pmm) REVERT: I 246 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8822 (tm-30) REVERT: I 273 LYS cc_start: 0.9508 (mttt) cc_final: 0.8938 (tmtt) REVERT: J 38 GLN cc_start: 0.8703 (tp40) cc_final: 0.8168 (tt0) REVERT: J 104 ASP cc_start: 0.9323 (t70) cc_final: 0.9012 (t0) REVERT: J 229 MET cc_start: 0.9135 (ptp) cc_final: 0.8580 (ppp) REVERT: J 230 LEU cc_start: 0.9838 (tt) cc_final: 0.9608 (mt) outliers start: 49 outliers final: 38 residues processed: 353 average time/residue: 0.1288 time to fit residues: 71.9225 Evaluate side-chains 347 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 307 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 245 ASP 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 199 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 269 GLN 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 248 LEU Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 133 LEU 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 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: 2.9990 chunk 189 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 168 optimal weight: 0.0050 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.104450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.072942 restraints weight = 63144.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075215 restraints weight = 34223.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076709 restraints weight = 23109.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077652 restraints weight = 17975.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.078237 restraints weight = 15350.371| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.6657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19279 Z= 0.134 Angle : 0.710 13.244 26167 Z= 0.358 Chirality : 0.044 0.264 2990 Planarity : 0.004 0.041 3205 Dihedral : 13.908 156.506 3019 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.57 % Allowed : 24.16 % Favored : 73.27 % 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: 0.92 (0.17), residues: 2338 helix: 1.11 (0.15), residues: 1300 sheet: -0.46 (0.53), residues: 96 loop : 0.19 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 231 TYR 0.016 0.001 TYR F 112 PHE 0.045 0.002 PHE I 125 TRP 0.017 0.001 TRP J 211 HIS 0.005 0.001 HIS F 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (19275) covalent geometry : angle 0.71039 / 0.36 (26167) hydrogen bonds : bond 0.04040 / 3.08 ( 903) hydrogen bonds : angle 4.61740 / 3.46 ( 2663) Misc. bond : bond 0.00121 / 0.06 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3854.09 seconds wall clock time: 67 minutes 13.00 seconds (4033.00 seconds total)