Starting phenix.real_space_refine on Sat Jul 4 19:09:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7svv_25454/07_2026/7svv_25454.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svv_25454/07_2026/7svv_25454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7svv_25454/07_2026/7svv_25454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svv_25454/07_2026/7svv_25454.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7svv_25454/07_2026/7svv_25454.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7svv_25454/07_2026/7svv_25454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7svv_25454/07_2026/7svv_25454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svv_25454/07_2026/7svv_25454.map" } resolution = 3.54 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= 0.004 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 68 5.49 5 Mg 10 5.21 5 S 80 5.16 5 C 14367 2.51 5 N 4153 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s 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: 23046 Number of models: 1 Model: "" Number of chains: 32 Chain: "1" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 380 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "2" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 2 Chain: "A" 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: "a" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "B" 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: "b" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} 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: "c" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} 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: "d" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} 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: "e" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} 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: "f" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} 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: "g" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} 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: "h" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 126 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: "i" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} 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: "j" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 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, 'ANP': 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, 'ANP': 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, 'ANP': 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, 'ANP': 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, 'ANP': 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, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.82, per 1000 atoms: 0.21 Number of scatterers: 23046 At special positions: 0 Unit cell: (142.31, 136.99, 135.66, 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 80 16.00 P 68 15.00 Mg 10 11.99 O 4368 8.00 N 4153 7.00 C 14367 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 883.8 milliseconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 20 sheets defined 61.7% alpha, 7.4% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.757A pdb=" N ARG A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 52 removed outlier: 3.568A pdb=" N LYS A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.544A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.092A pdb=" N ASP A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 200 through 215 Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.849A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 258 removed outlier: 3.546A pdb=" N GLU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'a' and resid 575 through 581 Processing helix chain 'B' and resid 20 through 29 removed outlier: 3.757A pdb=" N ARG B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 52 removed outlier: 3.568A pdb=" N LYS B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.543A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 173 through 181 removed outlier: 4.092A pdb=" N ASP B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 190 Processing helix chain 'B' and resid 200 through 215 Processing helix chain 'B' and resid 226 through 238 removed outlier: 3.849A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 258 removed outlier: 3.546A pdb=" N GLU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'b' and resid 575 through 581 Processing helix chain 'C' and resid 20 through 29 removed outlier: 3.757A pdb=" N ARG C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 52 removed outlier: 3.568A pdb=" N LYS C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 75 Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.543A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 Processing helix chain 'C' and resid 145 through 149 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 173 through 181 removed outlier: 4.092A pdb=" N ASP C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'C' and resid 200 through 215 Processing helix chain 'C' and resid 226 through 238 removed outlier: 3.849A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 258 removed outlier: 3.546A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'c' and resid 575 through 581 Processing helix chain 'D' and resid 20 through 29 removed outlier: 3.756A pdb=" N ARG D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 52 removed outlier: 3.568A pdb=" N LYS D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.544A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 134 Processing helix chain 'D' and resid 145 through 149 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 173 through 181 removed outlier: 4.091A pdb=" N ASP D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 200 through 215 Processing helix chain 'D' and resid 226 through 238 removed outlier: 3.849A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 removed outlier: 3.547A pdb=" N GLU D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 273 Processing helix chain 'd' and resid 575 through 581 Processing helix chain 'E' and resid 20 through 29 removed outlier: 3.757A pdb=" N ARG E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.567A pdb=" N LYS E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 75 Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.543A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 134 Processing helix chain 'E' and resid 145 through 149 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 173 through 181 removed outlier: 4.091A pdb=" N ASP E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 Processing helix chain 'E' and resid 200 through 215 Processing helix chain 'E' and resid 226 through 238 removed outlier: 3.850A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 258 removed outlier: 3.546A pdb=" N GLU E 246 " --> pdb=" O GLY E 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'e' and resid 575 through 581 Processing helix chain 'F' and resid 20 through 29 removed outlier: 3.756A pdb=" N ARG F 27 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 52 removed outlier: 3.568A pdb=" N LYS F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.544A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 134 Processing helix chain 'F' and resid 145 through 149 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 173 through 181 removed outlier: 4.092A pdb=" N ASP F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 200 through 215 Processing helix chain 'F' and resid 226 through 238 removed outlier: 3.850A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 258 removed outlier: 3.547A pdb=" N GLU F 246 " --> pdb=" O GLY F 242 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'f' and resid 575 through 581 Processing helix chain 'G' and resid 20 through 29 removed outlier: 3.757A pdb=" N ARG G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 52 removed outlier: 3.568A pdb=" N LYS G 51 " --> pdb=" O ASP G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 75 Processing helix chain 'G' and resid 101 through 113 removed outlier: 3.543A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 134 Processing helix chain 'G' and resid 145 through 149 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 173 through 181 removed outlier: 4.091A pdb=" N ASP G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 200 through 215 Processing helix chain 'G' and resid 226 through 238 removed outlier: 3.850A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 258 removed outlier: 3.547A pdb=" N GLU G 246 " --> pdb=" O GLY G 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'g' and resid 575 through 581 Processing helix chain 'H' and resid 20 through 29 removed outlier: 3.757A pdb=" N ARG H 27 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 52 removed outlier: 3.568A pdb=" N LYS H 51 " --> pdb=" O ASP H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 101 through 113 removed outlier: 3.544A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS H 107 " --> pdb=" O LYS H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 134 Processing helix chain 'H' and resid 145 through 149 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 173 through 181 removed outlier: 4.092A pdb=" N ASP H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 Processing helix chain 'H' and resid 200 through 215 Processing helix chain 'H' and resid 226 through 238 removed outlier: 3.850A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 258 removed outlier: 3.546A pdb=" N GLU H 246 " --> pdb=" O GLY H 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 273 Processing helix chain 'h' and resid 575 through 581 Processing helix chain 'I' and resid 20 through 29 removed outlier: 3.756A pdb=" N ARG I 27 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 52 removed outlier: 3.568A pdb=" N LYS I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 75 Processing helix chain 'I' and resid 101 through 113 removed outlier: 3.544A pdb=" N LEU I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 134 Processing helix chain 'I' and resid 145 through 149 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 173 through 181 removed outlier: 4.091A pdb=" N ASP I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 Processing helix chain 'I' and resid 200 through 215 Processing helix chain 'I' and resid 226 through 238 removed outlier: 3.849A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 258 removed outlier: 3.546A pdb=" N GLU I 246 " --> pdb=" O GLY I 242 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG I 258 " --> pdb=" O ARG I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'i' and resid 575 through 581 Processing helix chain 'J' and resid 20 through 29 removed outlier: 3.756A pdb=" N ARG J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 52 removed outlier: 3.568A pdb=" N LYS J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 75 Processing helix chain 'J' and resid 101 through 113 removed outlier: 3.544A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS J 107 " --> pdb=" O LYS J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 134 Processing helix chain 'J' and resid 145 through 149 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 173 through 181 removed outlier: 4.091A pdb=" N ASP J 177 " --> pdb=" O THR J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 Processing helix chain 'J' and resid 200 through 215 Processing helix chain 'J' and resid 226 through 238 removed outlier: 3.849A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 258 removed outlier: 3.546A pdb=" N GLU J 246 " --> pdb=" O GLY J 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG J 258 " --> pdb=" O ARG J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 273 Processing helix chain 'j' and resid 575 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.665A pdb=" N VAL A 92 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG A 57 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE A 196 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 59 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.664A pdb=" N VAL B 92 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG B 57 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE B 196 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 59 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA6, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.664A pdb=" N VAL C 92 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE C 196 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 59 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AA8, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.665A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG D 57 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE D 196 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL D 59 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AB1, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.665A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE E 196 " --> pdb=" O ARG E 57 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL E 59 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 32 through 33 Processing sheet with id=AB3, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.665A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG F 57 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE F 196 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL F 59 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AB5, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.665A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE G 196 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL G 59 " --> pdb=" O PHE G 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 32 through 33 Processing sheet with id=AB7, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.664A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE H 196 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL H 59 " --> pdb=" O PHE H 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 32 through 33 Processing sheet with id=AB9, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.665A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE I 196 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL I 59 " --> pdb=" O PHE I 196 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 32 through 33 Processing sheet with id=AC2, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.665A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE J 196 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL J 59 " --> pdb=" O PHE J 196 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 3213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3736 1.28 - 1.41: 5774 1.41 - 1.55: 13745 1.55 - 1.68: 92 1.68 - 1.81: 140 Bond restraints: 23487 Sorted by residual: bond pdb=" O3A ANP F 300 " pdb=" PB ANP F 300 " ideal model delta sigma weight residual 1.700 1.506 0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" O3A ANP E 300 " pdb=" PB ANP E 300 " ideal model delta sigma weight residual 1.700 1.506 0.194 2.00e-02 2.50e+03 9.41e+01 bond pdb=" O3A ANP G 300 " pdb=" PB ANP G 300 " ideal model delta sigma weight residual 1.700 1.538 0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" O3A ANP H 300 " pdb=" PB ANP H 300 " ideal model delta sigma weight residual 1.700 1.538 0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" O3A ANP J 300 " pdb=" PB ANP J 300 " ideal model delta sigma weight residual 1.700 1.540 0.160 2.00e-02 2.50e+03 6.43e+01 ... (remaining 23482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.39: 31179 5.39 - 10.78: 572 10.78 - 16.17: 24 16.17 - 21.56: 11 21.56 - 26.95: 13 Bond angle restraints: 31799 Sorted by residual: angle pdb=" N LYS I 265 " pdb=" CA LYS I 265 " pdb=" C LYS I 265 " ideal model delta sigma weight residual 111.07 120.80 -9.73 1.07e+00 8.73e-01 8.27e+01 angle pdb=" N LYS A 265 " pdb=" CA LYS A 265 " pdb=" C LYS A 265 " ideal model delta sigma weight residual 111.07 120.79 -9.72 1.07e+00 8.73e-01 8.25e+01 angle pdb=" N LYS E 265 " pdb=" CA LYS E 265 " pdb=" C LYS E 265 " ideal model delta sigma weight residual 111.07 120.79 -9.72 1.07e+00 8.73e-01 8.25e+01 angle pdb=" N LYS C 265 " pdb=" CA LYS C 265 " pdb=" C LYS C 265 " ideal model delta sigma weight residual 111.07 120.78 -9.71 1.07e+00 8.73e-01 8.23e+01 angle pdb=" N LYS G 265 " pdb=" CA LYS G 265 " pdb=" C LYS G 265 " ideal model delta sigma weight residual 111.07 120.78 -9.71 1.07e+00 8.73e-01 8.23e+01 ... (remaining 31794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 13922 34.93 - 69.85: 357 69.85 - 104.78: 20 104.78 - 139.71: 3 139.71 - 174.63: 10 Dihedral angle restraints: 14312 sinusoidal: 6452 harmonic: 7860 Sorted by residual: dihedral pdb=" C TYR h 582 " pdb=" N TYR h 582 " pdb=" CA TYR h 582 " pdb=" CB TYR h 582 " ideal model delta harmonic sigma weight residual -122.60 -137.09 14.49 0 2.50e+00 1.60e-01 3.36e+01 dihedral pdb=" C TYR a 582 " pdb=" N TYR a 582 " pdb=" CA TYR a 582 " pdb=" CB TYR a 582 " ideal model delta harmonic sigma weight residual -122.60 -137.09 14.49 0 2.50e+00 1.60e-01 3.36e+01 dihedral pdb=" C TYR e 582 " pdb=" N TYR e 582 " pdb=" CA TYR e 582 " pdb=" CB TYR e 582 " ideal model delta harmonic sigma weight residual -122.60 -137.08 14.48 0 2.50e+00 1.60e-01 3.36e+01 ... (remaining 14309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 3064 0.131 - 0.262: 410 0.262 - 0.394: 45 0.394 - 0.525: 2 0.525 - 0.656: 10 Chirality restraints: 3531 Sorted by residual: chirality pdb=" CA TYR a 582 " pdb=" N TYR a 582 " pdb=" C TYR a 582 " pdb=" CB TYR a 582 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA TYR h 582 " pdb=" N TYR h 582 " pdb=" C TYR h 582 " pdb=" CB TYR h 582 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA TYR d 582 " pdb=" N TYR d 582 " pdb=" C TYR d 582 " pdb=" CB TYR d 582 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 ... (remaining 3528 not shown) Planarity restraints: 3858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 255 " -0.030 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C SER J 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER J 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU J 256 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 255 " 0.030 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C SER A 255 " -0.103 2.00e-02 2.50e+03 pdb=" O SER A 255 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU A 256 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 255 " -0.030 2.00e-02 2.50e+03 5.94e-02 3.52e+01 pdb=" C SER B 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER B 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU B 256 " -0.036 2.00e-02 2.50e+03 ... (remaining 3855 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 15 2.04 - 2.75: 3822 2.75 - 3.47: 30806 3.47 - 4.18: 53047 4.18 - 4.90: 91984 Nonbonded interactions: 179674 Sorted by model distance: nonbonded pdb=" O1G ANP C 300 " pdb="MG MG C 301 " model vdw 1.320 2.170 nonbonded pdb=" O1G ANP G 300 " pdb="MG MG G 301 " model vdw 1.413 2.170 nonbonded pdb=" O1G ANP D 300 " pdb="MG MG D 301 " model vdw 1.557 2.170 nonbonded pdb=" O1G ANP A 300 " pdb="MG MG A 301 " model vdw 1.564 2.170 nonbonded pdb=" O1G ANP J 300 " pdb="MG MG J 301 " model vdw 1.567 2.170 ... (remaining 179669 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'a' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'b' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'c' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'd' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'e' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'f' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'g' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = chain 'h' selection = (chain 'i' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'j' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) } 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: 0.980 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.910 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.025 0.869 23496 Z= 1.980 Angle : 1.882 26.945 31799 Z= 1.309 Chirality : 0.101 0.656 3531 Planarity : 0.010 0.059 3858 Dihedral : 14.466 174.635 9232 Min Nonbonded Distance : 1.320 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.39 % 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: -0.21 (0.15), residues: 2670 helix: -0.55 (0.11), residues: 1560 sheet: 2.55 (0.30), residues: 230 loop : 0.25 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 249 TYR 0.016 0.002 TYR J 112 PHE 0.007 0.001 PHE E 196 TRP 0.012 0.002 TRP B 45 HIS 0.001 0.000 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.02037 / 1.43 (23487) covalent geometry : angle 1.88214 / 1.31 (31799) hydrogen bonds : bond 0.24473 / 25.05 ( 1147) hydrogen bonds : angle 7.91435 / 7.96 ( 3285) Misc. bond : bond 0.69749 / 58.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 718 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7512 (ttm110) REVERT: B 40 LYS cc_start: 0.8168 (tptp) cc_final: 0.7947 (ttmt) REVERT: B 47 ASP cc_start: 0.7479 (t70) cc_final: 0.7186 (t0) REVERT: B 54 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7566 (tttp) REVERT: B 188 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7878 (mm-30) REVERT: B 230 LEU cc_start: 0.8706 (mt) cc_final: 0.8354 (tp) REVERT: B 235 SER cc_start: 0.8612 (m) cc_final: 0.8247 (t) REVERT: B 268 LEU cc_start: 0.8973 (tp) cc_final: 0.8693 (tt) REVERT: D 159 ASP cc_start: 0.6235 (m-30) cc_final: 0.5657 (m-30) REVERT: D 229 MET cc_start: 0.8271 (mmm) cc_final: 0.7976 (mmt) REVERT: D 250 GLU cc_start: 0.7518 (tp30) cc_final: 0.7224 (tt0) REVERT: E 123 SER cc_start: 0.8818 (p) cc_final: 0.7493 (t) REVERT: F 47 ASP cc_start: 0.7944 (t70) cc_final: 0.7608 (t0) REVERT: F 54 LYS cc_start: 0.8306 (mmtm) cc_final: 0.7991 (tttm) REVERT: F 140 MET cc_start: 0.9285 (ttm) cc_final: 0.9047 (ttp) REVERT: F 159 ASP cc_start: 0.6987 (m-30) cc_final: 0.6533 (m-30) REVERT: F 163 ASP cc_start: 0.8125 (m-30) cc_final: 0.7855 (m-30) REVERT: F 229 MET cc_start: 0.8570 (mmm) cc_final: 0.8234 (mmm) REVERT: G 27 ARG cc_start: 0.7204 (ttp80) cc_final: 0.6763 (ptt90) REVERT: G 119 LYS cc_start: 0.6347 (tptp) cc_final: 0.6093 (tppt) REVERT: G 139 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8102 (mt-10) REVERT: G 162 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6053 (mm-30) REVERT: G 231 ARG cc_start: 0.7312 (ttm110) cc_final: 0.7110 (ttp80) REVERT: H 107 LYS cc_start: 0.8113 (tttm) cc_final: 0.7722 (mtmt) REVERT: H 140 MET cc_start: 0.9376 (ttm) cc_final: 0.9137 (ttm) REVERT: H 163 ASP cc_start: 0.7744 (m-30) cc_final: 0.7404 (m-30) REVERT: H 187 LEU cc_start: 0.8816 (tp) cc_final: 0.8563 (tt) REVERT: H 238 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7465 (mt-10) REVERT: h 582 TYR cc_start: 0.6758 (t80) cc_final: 0.6328 (t80) REVERT: I 76 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7395 (ttm-80) REVERT: I 238 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7808 (mt-10) REVERT: I 269 GLN cc_start: 0.7174 (mt0) cc_final: 0.6855 (tt0) REVERT: J 76 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7484 (mtt-85) REVERT: J 269 GLN cc_start: 0.7408 (mt0) cc_final: 0.7040 (mt0) outliers start: 0 outliers final: 0 residues processed: 718 average time/residue: 0.2236 time to fit residues: 223.6318 Evaluate side-chains 383 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 223 ASN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.115517 restraints weight = 30322.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117126 restraints weight = 31972.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117816 restraints weight = 25919.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118080 restraints weight = 22340.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118164 restraints weight = 20783.239| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23496 Z= 0.160 Angle : 0.656 7.496 31799 Z= 0.352 Chirality : 0.044 0.246 3531 Planarity : 0.005 0.052 3858 Dihedral : 15.470 179.639 3514 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.94 % Allowed : 8.65 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.16), residues: 2670 helix: 1.11 (0.13), residues: 1590 sheet: 2.93 (0.33), residues: 230 loop : -0.05 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 191 TYR 0.027 0.001 TYR a 575 PHE 0.014 0.002 PHE C 125 TRP 0.011 0.001 TRP J 45 HIS 0.004 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (23487) covalent geometry : angle 0.65635 / 0.35 (31799) hydrogen bonds : bond 0.05862 / 6.02 ( 1147) hydrogen bonds : angle 4.87812 / 4.73 ( 3285) Misc. bond : bond 0.00711 / 0.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 408 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7502 (tttm) cc_final: 0.6979 (ttpt) REVERT: A 127 ASP cc_start: 0.6798 (m-30) cc_final: 0.6569 (m-30) REVERT: B 188 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7748 (mm-30) REVERT: B 235 SER cc_start: 0.8288 (m) cc_final: 0.8056 (t) REVERT: B 265 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7786 (mmtt) REVERT: B 268 LEU cc_start: 0.8908 (tp) cc_final: 0.8666 (tt) REVERT: C 182 ARG cc_start: 0.7040 (ttm-80) cc_final: 0.6437 (ttp-110) REVERT: C 206 ASN cc_start: 0.7236 (m-40) cc_final: 0.7024 (m110) REVERT: D 229 MET cc_start: 0.8182 (mmm) cc_final: 0.7883 (mmt) REVERT: D 230 LEU cc_start: 0.8675 (mt) cc_final: 0.8396 (tp) REVERT: D 250 GLU cc_start: 0.7848 (tp30) cc_final: 0.7397 (tt0) REVERT: E 82 GLU cc_start: 0.5445 (pt0) cc_final: 0.5153 (pt0) REVERT: E 181 LYS cc_start: 0.7970 (mttt) cc_final: 0.7754 (mtmt) REVERT: E 210 MET cc_start: 0.8040 (ttm) cc_final: 0.7809 (ttm) REVERT: F 47 ASP cc_start: 0.7650 (t70) cc_final: 0.7287 (t0) REVERT: F 159 ASP cc_start: 0.7483 (m-30) cc_final: 0.6968 (m-30) REVERT: G 54 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7727 (mtpp) REVERT: G 119 LYS cc_start: 0.6548 (tptp) cc_final: 0.6120 (tppt) REVERT: G 162 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6439 (mm-30) REVERT: G 231 ARG cc_start: 0.7198 (ttm110) cc_final: 0.6831 (ttp80) REVERT: H 107 LYS cc_start: 0.8082 (tttm) cc_final: 0.7712 (ttmt) REVERT: H 163 ASP cc_start: 0.7986 (m-30) cc_final: 0.7731 (m-30) REVERT: I 225 LYS cc_start: 0.7330 (ttmt) cc_final: 0.7052 (tmtt) REVERT: I 227 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7099 (ptpt) REVERT: I 238 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7879 (mt-10) REVERT: i 582 TYR cc_start: 0.7025 (t80) cc_final: 0.6666 (t80) REVERT: J 47 ASP cc_start: 0.7371 (t70) cc_final: 0.7141 (t0) REVERT: J 76 ARG cc_start: 0.7751 (mtp180) cc_final: 0.7426 (mtt-85) REVERT: J 78 LYS cc_start: 0.7446 (mttt) cc_final: 0.7057 (mtpt) REVERT: J 181 LYS cc_start: 0.7231 (mttt) cc_final: 0.6926 (mttm) REVERT: J 269 GLN cc_start: 0.7417 (mt0) cc_final: 0.7188 (mt0) REVERT: J 270 GLU cc_start: 0.6679 (tp30) cc_final: 0.6438 (tp30) outliers start: 46 outliers final: 28 residues processed: 432 average time/residue: 0.1993 time to fit residues: 125.1235 Evaluate side-chains 370 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 340 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain b residue 578 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 255 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 119 optimal weight: 0.1980 chunk 180 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN A 80 GLN C 269 GLN E 269 GLN G 269 GLN I 37 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109641 restraints weight = 30342.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110933 restraints weight = 32673.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111391 restraints weight = 26606.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.112589 restraints weight = 23828.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112481 restraints weight = 20655.595| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23496 Z= 0.150 Angle : 0.588 8.593 31799 Z= 0.311 Chirality : 0.042 0.250 3531 Planarity : 0.005 0.051 3858 Dihedral : 15.518 177.916 3514 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.90 % Allowed : 9.92 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.16), residues: 2670 helix: 1.54 (0.13), residues: 1590 sheet: 2.53 (0.33), residues: 230 loop : -0.10 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 85 TYR 0.024 0.001 TYR a 575 PHE 0.008 0.001 PHE I 154 TRP 0.011 0.001 TRP J 45 HIS 0.005 0.001 HIS J 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (23487) covalent geometry : angle 0.58761 / 0.31 (31799) hydrogen bonds : bond 0.04571 / 4.70 ( 1147) hydrogen bonds : angle 4.51570 / 4.31 ( 3285) Misc. bond : bond 0.00569 / 0.43 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 358 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7588 (tttm) cc_final: 0.7133 (ttpt) REVERT: A 127 ASP cc_start: 0.7176 (m-30) cc_final: 0.6822 (m-30) REVERT: A 205 LYS cc_start: 0.8275 (tmmt) cc_final: 0.8045 (tptp) REVERT: B 211 TRP cc_start: 0.8657 (t-100) cc_final: 0.8317 (t-100) REVERT: B 235 SER cc_start: 0.8236 (m) cc_final: 0.8015 (t) REVERT: B 268 LEU cc_start: 0.8900 (tp) cc_final: 0.8676 (tt) REVERT: b 573 TRP cc_start: 0.7682 (m-10) cc_final: 0.7461 (m-10) REVERT: C 182 ARG cc_start: 0.7262 (ttm-80) cc_final: 0.6688 (ttp-110) REVERT: C 230 LEU cc_start: 0.8277 (mt) cc_final: 0.7998 (tp) REVERT: D 229 MET cc_start: 0.8323 (mmm) cc_final: 0.8021 (mmt) REVERT: D 230 LEU cc_start: 0.8530 (mt) cc_final: 0.8302 (tp) REVERT: D 250 GLU cc_start: 0.7864 (tp30) cc_final: 0.7502 (tt0) REVERT: E 181 LYS cc_start: 0.8297 (mttt) cc_final: 0.7909 (mtmt) REVERT: E 232 ILE cc_start: 0.8566 (mm) cc_final: 0.8354 (mm) REVERT: F 20 TRP cc_start: 0.7329 (OUTLIER) cc_final: 0.7007 (t-100) REVERT: F 159 ASP cc_start: 0.7651 (m-30) cc_final: 0.7085 (m-30) REVERT: F 255 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8284 (m) REVERT: f 579 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7522 (ttm170) REVERT: G 113 LEU cc_start: 0.8259 (mt) cc_final: 0.7915 (mt) REVERT: G 119 LYS cc_start: 0.6238 (tptp) cc_final: 0.5931 (tppt) REVERT: G 123 SER cc_start: 0.7670 (OUTLIER) cc_final: 0.7368 (m) REVERT: G 162 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6447 (mm-30) REVERT: G 231 ARG cc_start: 0.7270 (ttm110) cc_final: 0.6856 (ttp80) REVERT: H 163 ASP cc_start: 0.7945 (m-30) cc_final: 0.7647 (m-30) REVERT: H 203 ASP cc_start: 0.7985 (t0) cc_final: 0.7695 (t0) REVERT: I 238 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7913 (mt-10) REVERT: J 76 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7511 (mtt-85) REVERT: J 181 LYS cc_start: 0.7302 (mttt) cc_final: 0.7095 (mttm) REVERT: J 269 GLN cc_start: 0.7612 (mt0) cc_final: 0.7265 (mt0) outliers start: 45 outliers final: 22 residues processed: 378 average time/residue: 0.1939 time to fit residues: 107.3814 Evaluate side-chains 338 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 313 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 263 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 69 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 260 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 182 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... g 577 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.108112 restraints weight = 30201.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110260 restraints weight = 31761.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.110807 restraints weight = 24800.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111062 restraints weight = 20343.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111198 restraints weight = 19907.766| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23496 Z= 0.128 Angle : 0.542 6.668 31799 Z= 0.287 Chirality : 0.041 0.254 3531 Planarity : 0.004 0.037 3858 Dihedral : 15.471 177.762 3514 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.98 % Allowed : 11.57 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.16), residues: 2670 helix: 1.73 (0.13), residues: 1600 sheet: 2.28 (0.33), residues: 230 loop : -0.12 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 579 TYR 0.024 0.001 TYR j 575 PHE 0.006 0.001 PHE C 106 TRP 0.015 0.001 TRP G 20 HIS 0.003 0.001 HIS J 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (23487) covalent geometry : angle 0.54216 / 0.29 (31799) hydrogen bonds : bond 0.04018 / 4.14 ( 1147) hydrogen bonds : angle 4.36878 / 4.14 ( 3285) Misc. bond : bond 0.00373 / 0.26 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 326 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7590 (tttm) cc_final: 0.7047 (ttpt) REVERT: A 113 LEU cc_start: 0.8634 (mt) cc_final: 0.8226 (mt) REVERT: A 203 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7829 (t0) REVERT: A 205 LYS cc_start: 0.8300 (tmmt) cc_final: 0.8088 (tptp) REVERT: B 211 TRP cc_start: 0.8640 (t-100) cc_final: 0.8311 (t-100) REVERT: B 235 SER cc_start: 0.8261 (m) cc_final: 0.8034 (t) REVERT: C 182 ARG cc_start: 0.7155 (ttm-80) cc_final: 0.6579 (ttp-110) REVERT: C 230 LEU cc_start: 0.8215 (mt) cc_final: 0.8001 (tp) REVERT: D 203 ASP cc_start: 0.7618 (t0) cc_final: 0.7256 (t0) REVERT: D 229 MET cc_start: 0.8219 (mmm) cc_final: 0.7872 (mmt) REVERT: D 230 LEU cc_start: 0.8564 (mt) cc_final: 0.8362 (tp) REVERT: D 250 GLU cc_start: 0.7697 (tp30) cc_final: 0.7437 (tt0) REVERT: D 269 GLN cc_start: 0.7704 (mt0) cc_final: 0.7294 (mt0) REVERT: E 181 LYS cc_start: 0.8249 (mttt) cc_final: 0.7850 (mtmt) REVERT: F 159 ASP cc_start: 0.7640 (m-30) cc_final: 0.7275 (m-30) REVERT: F 255 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8292 (m) REVERT: G 113 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7820 (mt) REVERT: G 119 LYS cc_start: 0.6395 (tptp) cc_final: 0.6099 (tppt) REVERT: G 123 SER cc_start: 0.7457 (OUTLIER) cc_final: 0.7143 (m) REVERT: G 231 ARG cc_start: 0.7276 (ttm110) cc_final: 0.6846 (ttp80) REVERT: H 147 ASP cc_start: 0.7255 (p0) cc_final: 0.6989 (p0) REVERT: H 163 ASP cc_start: 0.8012 (m-30) cc_final: 0.7633 (m-30) REVERT: H 203 ASP cc_start: 0.7986 (t0) cc_final: 0.7710 (t0) REVERT: I 238 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7885 (mt-10) REVERT: I 269 GLN cc_start: 0.7566 (tt0) cc_final: 0.7281 (tt0) REVERT: J 269 GLN cc_start: 0.7655 (mt0) cc_final: 0.7378 (mt0) REVERT: J 270 GLU cc_start: 0.6419 (tp30) cc_final: 0.6185 (tp30) outliers start: 47 outliers final: 32 residues processed: 353 average time/residue: 0.1811 time to fit residues: 94.5147 Evaluate side-chains 337 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 301 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 246 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.106924 restraints weight = 30302.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.107932 restraints weight = 32750.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.108451 restraints weight = 26988.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109421 restraints weight = 24336.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109426 restraints weight = 21667.430| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23496 Z= 0.151 Angle : 0.562 7.759 31799 Z= 0.294 Chirality : 0.042 0.252 3531 Planarity : 0.004 0.035 3858 Dihedral : 15.539 178.635 3514 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.07 % Allowed : 12.41 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.16), residues: 2670 helix: 1.77 (0.13), residues: 1600 sheet: 2.09 (0.32), residues: 230 loop : -0.18 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 579 TYR 0.020 0.001 TYR a 575 PHE 0.008 0.001 PHE I 125 TRP 0.012 0.002 TRP G 20 HIS 0.006 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (23487) covalent geometry : angle 0.56227 / 0.29 (31799) hydrogen bonds : bond 0.04209 / 4.32 ( 1147) hydrogen bonds : angle 4.36925 / 4.14 ( 3285) Misc. bond : bond 0.00494 / 0.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 323 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7550 (tttm) cc_final: 0.7052 (ttpt) REVERT: A 113 LEU cc_start: 0.8711 (mt) cc_final: 0.8289 (mt) REVERT: A 127 ASP cc_start: 0.7047 (m-30) cc_final: 0.6645 (m-30) REVERT: A 203 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7797 (t0) REVERT: A 205 LYS cc_start: 0.8339 (tmmt) cc_final: 0.8042 (tptp) REVERT: B 211 TRP cc_start: 0.8665 (OUTLIER) cc_final: 0.8454 (t-100) REVERT: C 182 ARG cc_start: 0.7186 (ttm-80) cc_final: 0.6672 (ttp-110) REVERT: C 230 LEU cc_start: 0.8247 (mt) cc_final: 0.8016 (tp) REVERT: D 136 CYS cc_start: 0.6756 (t) cc_final: 0.6458 (t) REVERT: D 203 ASP cc_start: 0.7796 (t0) cc_final: 0.7393 (t0) REVERT: D 229 MET cc_start: 0.8275 (mmm) cc_final: 0.7952 (mmt) REVERT: D 230 LEU cc_start: 0.8526 (mt) cc_final: 0.8285 (tp) REVERT: D 250 GLU cc_start: 0.7795 (tp30) cc_final: 0.7469 (tt0) REVERT: D 269 GLN cc_start: 0.7673 (mt0) cc_final: 0.7429 (mt0) REVERT: E 214 MET cc_start: 0.6599 (ttm) cc_final: 0.6298 (ttm) REVERT: F 159 ASP cc_start: 0.7662 (m-30) cc_final: 0.7286 (m-30) REVERT: F 231 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7533 (mtm180) REVERT: F 255 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8250 (m) REVERT: G 113 LEU cc_start: 0.8379 (mt) cc_final: 0.8033 (mt) REVERT: G 119 LYS cc_start: 0.6524 (tptp) cc_final: 0.6128 (tppt) REVERT: G 123 SER cc_start: 0.7489 (OUTLIER) cc_final: 0.7171 (m) REVERT: G 231 ARG cc_start: 0.7454 (ttm110) cc_final: 0.7124 (ttp80) REVERT: G 269 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7755 (tp-100) REVERT: H 163 ASP cc_start: 0.8061 (m-30) cc_final: 0.7675 (m-30) REVERT: H 203 ASP cc_start: 0.7948 (t0) cc_final: 0.7729 (t0) REVERT: H 264 ASP cc_start: 0.7190 (p0) cc_final: 0.6757 (p0) REVERT: I 231 ARG cc_start: 0.7260 (ttm110) cc_final: 0.7033 (ttp-110) REVERT: I 238 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7883 (mt-10) REVERT: J 269 GLN cc_start: 0.7642 (mt0) cc_final: 0.7370 (mt0) REVERT: j 576 GLU cc_start: 0.8168 (tp30) cc_final: 0.7936 (tp30) outliers start: 49 outliers final: 32 residues processed: 355 average time/residue: 0.1871 time to fit residues: 99.3693 Evaluate side-chains 338 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 246 GLU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 246 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 190 optimal weight: 0.4980 chunk 147 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 97 HIS ** 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 = 0.3616 r_free = 0.3616 target = 0.140937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.107874 restraints weight = 30334.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109350 restraints weight = 31370.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110451 restraints weight = 25016.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110470 restraints weight = 21363.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.110542 restraints weight = 20492.668| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23496 Z= 0.121 Angle : 0.521 8.336 31799 Z= 0.276 Chirality : 0.041 0.255 3531 Planarity : 0.004 0.035 3858 Dihedral : 15.491 178.475 3514 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.94 % Allowed : 13.42 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.16), residues: 2670 helix: 1.90 (0.13), residues: 1600 sheet: 1.88 (0.28), residues: 280 loop : -0.18 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 579 TYR 0.024 0.001 TYR j 575 PHE 0.005 0.001 PHE A 106 TRP 0.014 0.001 TRP G 45 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (23487) covalent geometry : angle 0.52080 / 0.28 (31799) hydrogen bonds : bond 0.03716 / 3.82 ( 1147) hydrogen bonds : angle 4.30402 / 4.08 ( 3285) Misc. bond : bond 0.00249 / 0.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 334 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6639 (tt) REVERT: A 107 LYS cc_start: 0.7637 (tttm) cc_final: 0.7136 (ttpt) REVERT: A 113 LEU cc_start: 0.8662 (mt) cc_final: 0.8119 (mt) REVERT: A 203 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7803 (t0) REVERT: B 211 TRP cc_start: 0.8644 (OUTLIER) cc_final: 0.8412 (t-100) REVERT: C 182 ARG cc_start: 0.7203 (ttm-80) cc_final: 0.6679 (ttp-110) REVERT: C 230 LEU cc_start: 0.8218 (mt) cc_final: 0.7972 (tp) REVERT: D 136 CYS cc_start: 0.6678 (t) cc_final: 0.6418 (t) REVERT: D 203 ASP cc_start: 0.7823 (t0) cc_final: 0.7492 (t0) REVERT: D 229 MET cc_start: 0.8254 (mmm) cc_final: 0.7975 (mmt) REVERT: F 159 ASP cc_start: 0.7672 (m-30) cc_final: 0.7296 (m-30) REVERT: F 255 SER cc_start: 0.8950 (OUTLIER) cc_final: 0.8325 (m) REVERT: F 261 LYS cc_start: 0.6681 (mmtt) cc_final: 0.6344 (mtpt) REVERT: G 78 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7407 (mtpp) REVERT: G 113 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7978 (mt) REVERT: G 119 LYS cc_start: 0.6664 (tptp) cc_final: 0.6047 (tptm) REVERT: G 123 SER cc_start: 0.7491 (OUTLIER) cc_final: 0.7199 (m) REVERT: G 231 ARG cc_start: 0.7456 (ttm110) cc_final: 0.7024 (ttp80) REVERT: H 163 ASP cc_start: 0.8080 (m-30) cc_final: 0.7693 (m-30) REVERT: H 203 ASP cc_start: 0.7962 (t0) cc_final: 0.7753 (t0) REVERT: H 264 ASP cc_start: 0.7246 (p0) cc_final: 0.6862 (p0) REVERT: I 231 ARG cc_start: 0.7310 (ttm110) cc_final: 0.6862 (mtm-85) REVERT: I 238 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7866 (mt-10) REVERT: J 106 PHE cc_start: 0.8229 (m-80) cc_final: 0.7951 (m-80) outliers start: 46 outliers final: 30 residues processed: 361 average time/residue: 0.1886 time to fit residues: 102.3274 Evaluate side-chains 347 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 310 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain d residue 571 GLU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 152 GLU Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 246 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 225 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 185 optimal weight: 0.0870 chunk 240 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 ASN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.137825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.104697 restraints weight = 30178.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106313 restraints weight = 31893.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106896 restraints weight = 25022.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107046 restraints weight = 22246.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107123 restraints weight = 19986.118| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23496 Z= 0.180 Angle : 0.587 7.219 31799 Z= 0.305 Chirality : 0.043 0.252 3531 Planarity : 0.004 0.034 3858 Dihedral : 15.575 179.447 3514 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.94 % Allowed : 13.93 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.16), residues: 2670 helix: 1.74 (0.13), residues: 1600 sheet: 1.73 (0.28), residues: 280 loop : -0.30 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 85 TYR 0.020 0.001 TYR a 575 PHE 0.009 0.001 PHE D 106 TRP 0.015 0.002 TRP F 20 HIS 0.007 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (23487) covalent geometry : angle 0.58687 / 0.31 (31799) hydrogen bonds : bond 0.04423 / 4.51 ( 1147) hydrogen bonds : angle 4.37498 / 4.19 ( 3285) Misc. bond : bond 0.00429 / 0.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 332 time to evaluate : 0.928 Fit side-chains REVERT: A 21 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6759 (tt) REVERT: A 107 LYS cc_start: 0.7692 (tttm) cc_final: 0.7160 (ttpt) REVERT: A 113 LEU cc_start: 0.8745 (mt) cc_final: 0.8200 (mt) REVERT: A 116 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6561 (mmp80) REVERT: A 203 ASP cc_start: 0.8188 (m-30) cc_final: 0.7912 (t0) REVERT: A 205 LYS cc_start: 0.8642 (tptp) cc_final: 0.8338 (tptp) REVERT: B 211 TRP cc_start: 0.8683 (OUTLIER) cc_final: 0.8468 (t-100) REVERT: C 182 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.6739 (ttp-110) REVERT: C 230 LEU cc_start: 0.8271 (mt) cc_final: 0.8003 (tp) REVERT: D 136 CYS cc_start: 0.6566 (t) cc_final: 0.6356 (t) REVERT: D 203 ASP cc_start: 0.7887 (t0) cc_final: 0.7543 (t0) REVERT: D 229 MET cc_start: 0.8214 (mmm) cc_final: 0.7977 (mmt) REVERT: E 47 ASP cc_start: 0.8078 (t0) cc_final: 0.7841 (m-30) REVERT: E 159 ASP cc_start: 0.7656 (m-30) cc_final: 0.6999 (m-30) REVERT: E 181 LYS cc_start: 0.8233 (mttt) cc_final: 0.7782 (mtmt) REVERT: F 159 ASP cc_start: 0.7671 (m-30) cc_final: 0.7425 (m-30) REVERT: F 231 ARG cc_start: 0.7765 (mtm180) cc_final: 0.7563 (mtm180) REVERT: F 255 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8335 (m) REVERT: F 264 ASP cc_start: 0.6953 (p0) cc_final: 0.6491 (t0) REVERT: G 78 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7273 (mttm) REVERT: G 113 LEU cc_start: 0.8269 (mt) cc_final: 0.7912 (mt) REVERT: G 119 LYS cc_start: 0.6763 (tptp) cc_final: 0.6078 (tptm) REVERT: G 123 SER cc_start: 0.7546 (OUTLIER) cc_final: 0.7303 (m) REVERT: G 231 ARG cc_start: 0.7555 (ttm110) cc_final: 0.7044 (ttp80) REVERT: H 163 ASP cc_start: 0.8087 (m-30) cc_final: 0.7677 (m-30) REVERT: H 264 ASP cc_start: 0.7294 (p0) cc_final: 0.6954 (p0) REVERT: h 577 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7265 (tm-30) REVERT: I 231 ARG cc_start: 0.7364 (ttm110) cc_final: 0.6892 (mtm-85) REVERT: I 238 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7870 (mt-10) REVERT: J 64 THR cc_start: 0.8707 (p) cc_final: 0.8357 (p) outliers start: 46 outliers final: 35 residues processed: 363 average time/residue: 0.1940 time to fit residues: 104.6689 Evaluate side-chains 354 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 152 GLU Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 246 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 195 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 258 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 GLN G 98 GLN H 213 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105137 restraints weight = 30073.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106270 restraints weight = 31981.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106872 restraints weight = 26926.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107302 restraints weight = 24234.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107416 restraints weight = 22127.007| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23496 Z= 0.159 Angle : 0.560 7.240 31799 Z= 0.295 Chirality : 0.042 0.255 3531 Planarity : 0.004 0.042 3858 Dihedral : 15.565 179.675 3514 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.03 % Allowed : 14.44 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.16), residues: 2670 helix: 1.73 (0.13), residues: 1620 sheet: 1.69 (0.28), residues: 280 loop : -0.29 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG d 579 TYR 0.015 0.001 TYR a 575 PHE 0.007 0.001 PHE C 125 TRP 0.014 0.002 TRP C 45 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (23487) covalent geometry : angle 0.55987 / 0.29 (31799) hydrogen bonds : bond 0.04166 / 4.27 ( 1147) hydrogen bonds : angle 4.33735 / 4.16 ( 3285) Misc. bond : bond 0.00335 / 0.27 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 318 time to evaluate : 0.896 Fit side-chains REVERT: A 21 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6671 (tt) REVERT: A 107 LYS cc_start: 0.7709 (tttm) cc_final: 0.7236 (ttpt) REVERT: A 113 LEU cc_start: 0.8679 (mt) cc_final: 0.8195 (mt) REVERT: A 203 ASP cc_start: 0.8266 (m-30) cc_final: 0.7936 (t0) REVERT: B 211 TRP cc_start: 0.8685 (OUTLIER) cc_final: 0.8465 (t-100) REVERT: B 229 MET cc_start: 0.7113 (mmt) cc_final: 0.6846 (mmt) REVERT: C 182 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.6740 (ttp-110) REVERT: C 230 LEU cc_start: 0.8260 (mt) cc_final: 0.7962 (tp) REVERT: D 203 ASP cc_start: 0.7922 (t0) cc_final: 0.7588 (t0) REVERT: E 47 ASP cc_start: 0.8074 (t0) cc_final: 0.7851 (m-30) REVERT: E 159 ASP cc_start: 0.7673 (m-30) cc_final: 0.6979 (m-30) REVERT: E 181 LYS cc_start: 0.8255 (mttt) cc_final: 0.7775 (mtmt) REVERT: E 214 MET cc_start: 0.6808 (mtp) cc_final: 0.6476 (ttm) REVERT: F 159 ASP cc_start: 0.7688 (m-30) cc_final: 0.7365 (m-30) REVERT: F 231 ARG cc_start: 0.7559 (mtm180) cc_final: 0.7342 (mtm180) REVERT: F 264 ASP cc_start: 0.7032 (p0) cc_final: 0.6693 (t0) REVERT: G 113 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7929 (mt) REVERT: G 119 LYS cc_start: 0.6509 (tptp) cc_final: 0.5885 (tptm) REVERT: G 123 SER cc_start: 0.7707 (OUTLIER) cc_final: 0.7492 (m) REVERT: G 231 ARG cc_start: 0.7594 (ttm110) cc_final: 0.7053 (ttp80) REVERT: H 163 ASP cc_start: 0.8110 (m-30) cc_final: 0.7709 (m-30) REVERT: H 213 GLN cc_start: 0.7764 (tt0) cc_final: 0.7556 (tt0) REVERT: h 577 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7475 (tm-30) REVERT: I 223 ASN cc_start: 0.6707 (p0) cc_final: 0.6492 (p0) REVERT: I 231 ARG cc_start: 0.7381 (ttm110) cc_final: 0.7084 (ttp-110) REVERT: I 238 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7858 (mt-10) REVERT: J 20 TRP cc_start: 0.7144 (t60) cc_final: 0.6855 (t60) REVERT: J 64 THR cc_start: 0.8765 (p) cc_final: 0.8434 (p) REVERT: J 160 ILE cc_start: 0.8777 (mt) cc_final: 0.8293 (mm) outliers start: 48 outliers final: 34 residues processed: 350 average time/residue: 0.1801 time to fit residues: 94.5544 Evaluate side-chains 346 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain h residue 572 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 152 GLU Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 184 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 103 optimal weight: 0.7980 chunk 156 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 GLN F 206 ASN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106423 restraints weight = 30262.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.107386 restraints weight = 31925.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108015 restraints weight = 27480.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.108451 restraints weight = 24259.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.108571 restraints weight = 22410.166| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23496 Z= 0.130 Angle : 0.542 7.459 31799 Z= 0.286 Chirality : 0.041 0.256 3531 Planarity : 0.004 0.035 3858 Dihedral : 15.558 179.736 3514 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.48 % Allowed : 14.94 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.16), residues: 2670 helix: 1.81 (0.13), residues: 1620 sheet: 1.70 (0.28), residues: 280 loop : -0.22 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG d 579 TYR 0.014 0.001 TYR d 575 PHE 0.006 0.001 PHE C 125 TRP 0.015 0.001 TRP C 45 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (23487) covalent geometry : angle 0.54153 / 0.29 (31799) hydrogen bonds : bond 0.03850 / 3.92 ( 1147) hydrogen bonds : angle 4.29753 / 4.12 ( 3285) Misc. bond : bond 0.00262 / 0.22 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 321 time to evaluate : 0.931 Fit side-chains REVERT: A 21 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6661 (tt) REVERT: A 107 LYS cc_start: 0.7727 (tttm) cc_final: 0.7239 (ttpt) REVERT: A 113 LEU cc_start: 0.8605 (mt) cc_final: 0.8106 (mt) REVERT: A 203 ASP cc_start: 0.8241 (m-30) cc_final: 0.7699 (t0) REVERT: A 208 VAL cc_start: 0.9331 (t) cc_final: 0.9112 (p) REVERT: B 211 TRP cc_start: 0.8676 (OUTLIER) cc_final: 0.8448 (t-100) REVERT: C 182 ARG cc_start: 0.7342 (ttm-80) cc_final: 0.6748 (ttp-110) REVERT: C 230 LEU cc_start: 0.8247 (mt) cc_final: 0.7964 (tp) REVERT: D 203 ASP cc_start: 0.7916 (t0) cc_final: 0.7591 (t0) REVERT: E 47 ASP cc_start: 0.8070 (t0) cc_final: 0.7853 (m-30) REVERT: E 159 ASP cc_start: 0.7777 (m-30) cc_final: 0.6988 (m-30) REVERT: E 181 LYS cc_start: 0.8216 (mttt) cc_final: 0.7745 (mtmt) REVERT: E 214 MET cc_start: 0.6902 (mtp) cc_final: 0.6597 (ttm) REVERT: E 229 MET cc_start: 0.7691 (mmt) cc_final: 0.7463 (mtt) REVERT: F 159 ASP cc_start: 0.7679 (m-30) cc_final: 0.7215 (m-30) REVERT: F 231 ARG cc_start: 0.7555 (mtm180) cc_final: 0.7334 (mtm180) REVERT: F 264 ASP cc_start: 0.6975 (p0) cc_final: 0.6617 (t0) REVERT: G 113 LEU cc_start: 0.8226 (mt) cc_final: 0.7890 (mt) REVERT: G 119 LYS cc_start: 0.6645 (tptp) cc_final: 0.6034 (tptm) REVERT: G 231 ARG cc_start: 0.7580 (ttm110) cc_final: 0.7045 (ttp80) REVERT: H 163 ASP cc_start: 0.8118 (m-30) cc_final: 0.7664 (m-30) REVERT: H 213 GLN cc_start: 0.7827 (tt0) cc_final: 0.7540 (tt0) REVERT: H 231 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7589 (tpp80) REVERT: H 264 ASP cc_start: 0.7381 (p0) cc_final: 0.7112 (p0) REVERT: h 577 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7484 (tm-30) REVERT: I 223 ASN cc_start: 0.6739 (p0) cc_final: 0.6479 (p0) REVERT: I 231 ARG cc_start: 0.7341 (ttm110) cc_final: 0.6948 (mtm-85) REVERT: I 238 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7837 (mt-10) REVERT: J 20 TRP cc_start: 0.7149 (t60) cc_final: 0.6866 (t60) REVERT: J 64 THR cc_start: 0.8738 (p) cc_final: 0.8405 (p) outliers start: 35 outliers final: 30 residues processed: 345 average time/residue: 0.1866 time to fit residues: 96.7316 Evaluate side-chains 343 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 311 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 152 GLU Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 184 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 43 optimal weight: 0.6980 chunk 196 optimal weight: 0.2980 chunk 230 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 144 optimal weight: 0.0870 chunk 193 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 ASN D 269 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.141070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108195 restraints weight = 30031.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109250 restraints weight = 32775.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109720 restraints weight = 26858.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110568 restraints weight = 23687.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110564 restraints weight = 21467.991| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 23496 Z= 0.103 Angle : 0.514 9.404 31799 Z= 0.273 Chirality : 0.040 0.255 3531 Planarity : 0.003 0.036 3858 Dihedral : 15.514 179.491 3514 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.14 % Allowed : 15.32 % Favored : 83.54 % 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: 2.01 (0.16), residues: 2670 helix: 1.94 (0.13), residues: 1620 sheet: 1.75 (0.27), residues: 280 loop : -0.10 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG j 579 TYR 0.014 0.001 TYR j 575 PHE 0.006 0.001 PHE A 106 TRP 0.021 0.002 TRP e 573 HIS 0.003 0.000 HIS I 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (23487) covalent geometry : angle 0.51390 / 0.27 (31799) hydrogen bonds : bond 0.03296 / 3.36 ( 1147) hydrogen bonds : angle 4.25526 / 4.05 ( 3285) Misc. bond : bond 0.00198 / 0.16 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 328 time to evaluate : 0.933 Fit side-chains REVERT: A 21 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6640 (tt) REVERT: A 107 LYS cc_start: 0.7747 (tttm) cc_final: 0.7166 (ttpt) REVERT: A 113 LEU cc_start: 0.8577 (mt) cc_final: 0.8106 (mt) REVERT: A 208 VAL cc_start: 0.9365 (t) cc_final: 0.9152 (p) REVERT: B 211 TRP cc_start: 0.8660 (t-100) cc_final: 0.8446 (t-100) REVERT: C 182 ARG cc_start: 0.7339 (ttm-80) cc_final: 0.6730 (ttp-110) REVERT: C 230 LEU cc_start: 0.8243 (mt) cc_final: 0.8015 (tp) REVERT: D 203 ASP cc_start: 0.7865 (t0) cc_final: 0.7584 (t0) REVERT: E 159 ASP cc_start: 0.7642 (m-30) cc_final: 0.6935 (m-30) REVERT: E 181 LYS cc_start: 0.8132 (mttt) cc_final: 0.7698 (mtmt) REVERT: E 229 MET cc_start: 0.7630 (mmt) cc_final: 0.7420 (mtt) REVERT: F 159 ASP cc_start: 0.7519 (m-30) cc_final: 0.7032 (m-30) REVERT: F 231 ARG cc_start: 0.7535 (mtm180) cc_final: 0.7321 (mtm180) REVERT: F 264 ASP cc_start: 0.6961 (p0) cc_final: 0.6743 (t0) REVERT: G 62 SER cc_start: 0.8319 (t) cc_final: 0.8043 (m) REVERT: G 113 LEU cc_start: 0.8162 (mt) cc_final: 0.7813 (mt) REVERT: G 210 MET cc_start: 0.7685 (ttt) cc_final: 0.7208 (ttt) REVERT: G 231 ARG cc_start: 0.7502 (ttm110) cc_final: 0.6994 (ttp80) REVERT: H 163 ASP cc_start: 0.8123 (m-30) cc_final: 0.7681 (m-30) REVERT: H 203 ASP cc_start: 0.8032 (t0) cc_final: 0.7753 (t0) REVERT: H 264 ASP cc_start: 0.7346 (p0) cc_final: 0.7109 (p0) REVERT: h 577 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7506 (tm-30) REVERT: I 223 ASN cc_start: 0.6796 (p0) cc_final: 0.6562 (p0) REVERT: I 231 ARG cc_start: 0.7256 (ttm110) cc_final: 0.6916 (mtm-85) REVERT: I 238 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7870 (mt-10) REVERT: I 261 LYS cc_start: 0.7271 (mmtt) cc_final: 0.6953 (mmtm) REVERT: J 20 TRP cc_start: 0.7145 (t60) cc_final: 0.6849 (t60) REVERT: J 85 ARG cc_start: 0.6393 (mmt90) cc_final: 0.5826 (mtp180) REVERT: J 140 MET cc_start: 0.9209 (ttp) cc_final: 0.8908 (ttm) outliers start: 27 outliers final: 19 residues processed: 347 average time/residue: 0.1817 time to fit residues: 94.2603 Evaluate side-chains 337 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 317 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 152 GLU Chi-restraints excluded: chain J residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 96 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 ASN D 269 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107587 restraints weight = 30039.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108544 restraints weight = 32193.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109750 restraints weight = 27431.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109833 restraints weight = 22800.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109954 restraints weight = 21429.552| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23496 Z= 0.120 Angle : 0.527 7.839 31799 Z= 0.278 Chirality : 0.041 0.253 3531 Planarity : 0.004 0.035 3858 Dihedral : 15.540 179.131 3514 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.10 % Allowed : 16.00 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.16), residues: 2670 helix: 1.92 (0.13), residues: 1620 sheet: 1.71 (0.27), residues: 280 loop : -0.07 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG d 579 TYR 0.019 0.001 TYR j 575 PHE 0.011 0.001 PHE J 106 TRP 0.016 0.001 TRP C 45 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (23487) covalent geometry : angle 0.52695 / 0.28 (31799) hydrogen bonds : bond 0.03528 / 3.59 ( 1147) hydrogen bonds : angle 4.26924 / 4.09 ( 3285) Misc. bond : bond 0.00256 / 0.21 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3570.53 seconds wall clock time: 62 minutes 42.89 seconds (3762.89 seconds total)