Starting phenix.real_space_refine on Sun Sep 13 11:09:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7svv_25454/09_2026/7svv_25454.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svv_25454/09_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_25454/09_2026/7svv_25454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svv_25454/09_2026/7svv_25454.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7svv_25454/09_2026/7svv_25454.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7svv_25454/09_2026/7svv_25454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7svv_25454/09_2026/7svv_25454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svv_25454/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.42, per 1000 atoms: 0.24 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: 4.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.98 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: 4.25 Time building geometry restraints manager: 2.45 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: 1.660 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.360 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- 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 1.88231 / 1.31 (31799) hydrogen bonds : bond 0.24473 / 25.12 ( 1147) hydrogen bonds : angle 7.91435 / 7.97 ( 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 : 0.854 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: 0.7877 (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: 0.7990 (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: 0.6086 (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: 0.2074 time to fit residues: 208.1197 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 : 0.901 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.148244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.115537 restraints weight = 30280.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117144 restraints weight = 32289.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117768 restraints weight = 26366.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117956 restraints weight = 22408.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.118001 restraints weight = 21164.576| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3139 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= 0.165 Angle : 0.665 7.043 31799 Z= 0.353 Chirality : 0.044 0.271 3531 Planarity : 0.005 0.055 3858 Dihedral : 15.456 179.848 3514 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 1.30 (0.16), residues: 2670 helix: 1.10 (0.13), residues: 1590 sheet: 2.92 (0.33), residues: 230 loop : -0.06 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 191 TYR 0.024 0.002 TYR a 575 PHE 0.013 0.002 PHE C 125 TRP 0.012 0.002 TRP J 45 HIS 0.004 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (23487) covalent geometry : angle 0.66526 / 0.35 (31799) hydrogen bonds : bond 0.05590 / 5.75 ( 1147) hydrogen bonds : angle 4.85021 / 4.70 ( 3285) Misc. bond : bond 0.00534 / 0.44 ( 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 456 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 410 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7504 (tttm) cc_final: 0.7020 (ttpt) REVERT: A 127 ASP cc_start: 0.6866 (m-30) cc_final: 0.6647 (m-30) REVERT: B 188 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 235 SER cc_start: 0.8283 (m) cc_final: 0.8051 (t) REVERT: B 268 LEU cc_start: 0.8910 (tp) cc_final: 0.8667 (tt) REVERT: C 182 ARG cc_start: 0.7042 (ttm-80) cc_final: 0.6437 (ttp-110) REVERT: D 229 MET cc_start: 0.8175 (mmm) cc_final: 0.7893 (mmt) REVERT: D 230 LEU cc_start: 0.8673 (mt) cc_final: 0.8388 (tp) REVERT: D 250 GLU cc_start: 0.7836 (tp30) cc_final: 0.7391 (tt0) REVERT: E 82 GLU cc_start: 0.5603 (pt0) cc_final: 0.5320 (pt0) REVERT: E 181 LYS cc_start: 0.7984 (mttt) cc_final: 0.7757 (mtmt) REVERT: F 47 ASP cc_start: 0.7652 (t70) cc_final: 0.7300 (t0) REVERT: F 159 ASP cc_start: 0.7496 (m-30) cc_final: 0.6886 (m-30) REVERT: G 54 LYS cc_start: 0.7996 (mmtm) cc_final: 0.7712 (mtpp) REVERT: G 119 LYS cc_start: 0.6543 (tptp) cc_final: 0.6121 (tppt) REVERT: G 162 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6435 (mm-30) REVERT: G 231 ARG cc_start: 0.7197 (ttm110) cc_final: 0.6817 (ttp80) REVERT: H 107 LYS cc_start: 0.8077 (tttm) cc_final: 0.7705 (ttmt) REVERT: H 163 ASP cc_start: 0.7989 (m-30) cc_final: 0.7744 (m-30) REVERT: I 225 LYS cc_start: 0.7320 (ttmt) cc_final: 0.6983 (tmtt) REVERT: I 229 MET cc_start: 0.8247 (mmm) cc_final: 0.8028 (mmm) REVERT: I 238 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7894 (mt-10) REVERT: i 582 TYR cc_start: 0.7041 (t80) cc_final: 0.6692 (t80) REVERT: J 47 ASP cc_start: 0.7379 (t70) cc_final: 0.7147 (t0) REVERT: J 76 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7425 (mtt-85) REVERT: J 78 LYS cc_start: 0.7459 (mttt) cc_final: 0.7075 (mtpt) REVERT: J 181 LYS cc_start: 0.7238 (mttt) cc_final: 0.6966 (mttm) REVERT: J 269 GLN cc_start: 0.7423 (mt0) cc_final: 0.7196 (mt0) REVERT: J 270 GLU cc_start: 0.6709 (tp30) cc_final: 0.6460 (tp30) outliers start: 46 outliers final: 29 residues processed: 434 average time/residue: 0.1883 time to fit residues: 119.1830 Evaluate side-chains 368 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 339 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 180 ILE Chi-restraints excluded: chain E residue 235 SER 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 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 114 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: 0.9980 chunk 72 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 180 optimal weight: 0.1980 chunk 178 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 97 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.145038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.111659 restraints weight = 30286.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113056 restraints weight = 32641.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113756 restraints weight = 25525.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113987 restraints weight = 22405.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114452 restraints weight = 20361.908| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23496 Z= 0.128 Angle : 0.559 6.879 31799 Z= 0.298 Chirality : 0.041 0.276 3531 Planarity : 0.004 0.042 3858 Dihedral : 15.479 179.016 3514 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.69 % Allowed : 9.88 % Favored : 88.43 % 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: 1.74 (0.16), residues: 2670 helix: 1.60 (0.13), residues: 1590 sheet: 2.62 (0.33), residues: 230 loop : -0.04 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 85 TYR 0.022 0.001 TYR a 575 PHE 0.006 0.001 PHE A 106 TRP 0.011 0.001 TRP J 45 HIS 0.004 0.001 HIS J 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (23487) covalent geometry : angle 0.55936 / 0.30 (31799) hydrogen bonds : bond 0.04379 / 4.52 ( 1147) hydrogen bonds : angle 4.51315 / 4.31 ( 3285) Misc. bond : bond 0.00519 / 0.47 ( 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 396 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 356 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7585 (tttm) cc_final: 0.7075 (ttpt) REVERT: A 127 ASP cc_start: 0.7152 (m-30) cc_final: 0.6795 (m-30) REVERT: A 205 LYS cc_start: 0.8301 (tmmt) cc_final: 0.8027 (tptp) REVERT: B 188 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 211 TRP cc_start: 0.8632 (t-100) cc_final: 0.8315 (t-100) REVERT: B 235 SER cc_start: 0.8202 (m) cc_final: 0.7988 (t) REVERT: B 268 LEU cc_start: 0.8896 (tp) cc_final: 0.8693 (tt) REVERT: C 182 ARG cc_start: 0.7234 (ttm-80) cc_final: 0.6641 (ttp-110) REVERT: C 230 LEU cc_start: 0.8194 (mt) cc_final: 0.7903 (tp) REVERT: D 229 MET cc_start: 0.8259 (mmm) cc_final: 0.7951 (mmt) REVERT: D 230 LEU cc_start: 0.8678 (mt) cc_final: 0.8355 (tp) REVERT: D 250 GLU cc_start: 0.7843 (tp30) cc_final: 0.7526 (tt0) REVERT: E 113 LEU cc_start: 0.8083 (mt) cc_final: 0.7704 (mt) REVERT: E 181 LYS cc_start: 0.8254 (mttt) cc_final: 0.7890 (mtmt) REVERT: E 210 MET cc_start: 0.8061 (ttm) cc_final: 0.7686 (ttm) REVERT: E 232 ILE cc_start: 0.8546 (mm) cc_final: 0.8335 (mm) REVERT: F 159 ASP cc_start: 0.7625 (m-30) cc_final: 0.7011 (m-30) REVERT: F 255 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8250 (m) REVERT: f 579 ARG cc_start: 0.7851 (ttp-110) cc_final: 0.7437 (ttm170) REVERT: G 113 LEU cc_start: 0.8161 (mt) cc_final: 0.7630 (mt) REVERT: G 119 LYS cc_start: 0.6203 (tptp) cc_final: 0.5948 (tppt) REVERT: G 162 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6539 (mm-30) REVERT: G 231 ARG cc_start: 0.7219 (ttm110) cc_final: 0.6795 (ttp80) REVERT: H 163 ASP cc_start: 0.7932 (m-30) cc_final: 0.7585 (m-30) REVERT: H 203 ASP cc_start: 0.7986 (t0) cc_final: 0.7687 (t0) REVERT: I 238 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7866 (mt-10) REVERT: I 269 GLN cc_start: 0.7644 (mt0) cc_final: 0.7353 (tt0) REVERT: J 76 ARG cc_start: 0.7771 (mtp180) cc_final: 0.7473 (mtt-85) REVERT: J 181 LYS cc_start: 0.7510 (mttt) cc_final: 0.7258 (mttm) REVERT: J 269 GLN cc_start: 0.7520 (mt0) cc_final: 0.7195 (mt0) REVERT: J 270 GLU cc_start: 0.6661 (tp30) cc_final: 0.6391 (tp30) outliers start: 40 outliers final: 24 residues processed: 375 average time/residue: 0.2025 time to fit residues: 111.8139 Evaluate side-chains 343 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 318 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 28 LEU 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 e residue 581 GLU 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 J residue 81 GLN Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 246 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 69 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 260 optimal weight: 0.0570 chunk 126 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 GLN g 577 GLN I 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.107980 restraints weight = 30373.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108948 restraints weight = 31940.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.109922 restraints weight = 26370.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110169 restraints weight = 23424.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.110402 restraints weight = 22221.571| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23496 Z= 0.155 Angle : 0.575 6.578 31799 Z= 0.300 Chirality : 0.042 0.279 3531 Planarity : 0.004 0.036 3858 Dihedral : 15.467 177.373 3514 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.11 % Allowed : 11.69 % Favored : 86.20 % 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: 1.67 (0.13), residues: 1600 sheet: 2.32 (0.32), residues: 230 loop : -0.18 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG i 579 TYR 0.024 0.001 TYR j 575 PHE 0.007 0.001 PHE C 125 TRP 0.015 0.001 TRP G 20 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (23487) covalent geometry : angle 0.57461 / 0.30 (31799) hydrogen bonds : bond 0.04356 / 4.49 ( 1147) hydrogen bonds : angle 4.41434 / 4.20 ( 3285) Misc. bond : bond 0.00413 / 0.37 ( 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 383 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 333 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7599 (tttm) cc_final: 0.7086 (ttpt) REVERT: A 113 LEU cc_start: 0.8664 (mt) cc_final: 0.8250 (mt) REVERT: A 205 LYS cc_start: 0.8297 (tmmt) cc_final: 0.8089 (tptp) REVERT: B 211 TRP cc_start: 0.8648 (t-100) cc_final: 0.8322 (t-100) REVERT: B 235 SER cc_start: 0.8271 (m) cc_final: 0.8043 (t) REVERT: B 268 LEU cc_start: 0.8973 (tp) cc_final: 0.8747 (tt) REVERT: C 182 ARG cc_start: 0.7274 (ttm-80) cc_final: 0.6709 (ttp-110) REVERT: C 230 LEU cc_start: 0.8211 (mt) cc_final: 0.7948 (tp) REVERT: D 203 ASP cc_start: 0.7643 (t0) cc_final: 0.7268 (t0) REVERT: D 229 MET cc_start: 0.8238 (mmm) cc_final: 0.7916 (mmt) REVERT: D 250 GLU cc_start: 0.7709 (tp30) cc_final: 0.7435 (tt0) REVERT: D 269 GLN cc_start: 0.7647 (mt0) cc_final: 0.7184 (mt0) REVERT: E 210 MET cc_start: 0.8080 (ttm) cc_final: 0.7626 (ttm) REVERT: E 214 MET cc_start: 0.6642 (tpp) cc_final: 0.6363 (ttm) REVERT: F 159 ASP cc_start: 0.7643 (m-30) cc_final: 0.7271 (m-30) REVERT: F 255 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8295 (m) REVERT: G 113 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8003 (mt) REVERT: G 119 LYS cc_start: 0.6635 (tptp) cc_final: 0.6255 (tppt) REVERT: G 123 SER cc_start: 0.7476 (OUTLIER) cc_final: 0.7147 (m) REVERT: G 159 ASP cc_start: 0.7792 (m-30) cc_final: 0.7551 (m-30) REVERT: G 231 ARG cc_start: 0.7289 (ttm110) cc_final: 0.6883 (ttp80) REVERT: H 163 ASP cc_start: 0.8060 (m-30) cc_final: 0.7683 (m-30) REVERT: H 203 ASP cc_start: 0.8011 (t0) cc_final: 0.7727 (t0) REVERT: I 238 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7890 (mt-10) REVERT: J 268 LEU cc_start: 0.8388 (tp) cc_final: 0.8156 (tp) REVERT: J 269 GLN cc_start: 0.7722 (mt0) cc_final: 0.7426 (mt0) outliers start: 50 outliers final: 35 residues processed: 359 average time/residue: 0.1970 time to fit residues: 105.5361 Evaluate side-chains 344 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER 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 117 VAL Chi-restraints excluded: chain B residue 255 SER 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 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 113 LEU 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 253 ILE 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 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 Chi-restraints excluded: chain J residue 253 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 19 optimal weight: 0.0000 chunk 159 optimal weight: 3.9990 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: 0.8980 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... g 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108059 restraints weight = 30156.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.109706 restraints weight = 31865.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110327 restraints weight = 24285.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110372 restraints weight = 22074.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110633 restraints weight = 20166.569| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23496 Z= 0.133 Angle : 0.540 6.315 31799 Z= 0.285 Chirality : 0.041 0.282 3531 Planarity : 0.004 0.036 3858 Dihedral : 15.459 177.577 3514 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.98 % Allowed : 12.75 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.16), residues: 2670 helix: 1.80 (0.13), residues: 1600 sheet: 2.13 (0.32), residues: 230 loop : -0.16 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 579 TYR 0.024 0.001 TYR a 575 PHE 0.007 0.001 PHE H 190 TRP 0.013 0.001 TRP G 45 HIS 0.004 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (23487) covalent geometry : angle 0.54007 / 0.29 (31799) hydrogen bonds : bond 0.03966 / 4.09 ( 1147) hydrogen bonds : angle 4.33960 / 4.11 ( 3285) Misc. bond : bond 0.00351 / 0.30 ( 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 370 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 323 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7521 (tttm) cc_final: 0.7013 (ttpt) REVERT: A 113 LEU cc_start: 0.8670 (mt) cc_final: 0.8087 (mt) REVERT: B 211 TRP cc_start: 0.8661 (t-100) cc_final: 0.8324 (t-100) REVERT: B 235 SER cc_start: 0.8313 (m) cc_final: 0.8073 (t) REVERT: C 182 ARG cc_start: 0.7122 (ttm-80) cc_final: 0.6627 (ttp-110) REVERT: C 230 LEU cc_start: 0.8238 (mt) cc_final: 0.7963 (tp) REVERT: D 203 ASP cc_start: 0.7759 (t0) cc_final: 0.7377 (t0) REVERT: D 229 MET cc_start: 0.8206 (mmm) cc_final: 0.7908 (mmt) REVERT: D 230 LEU cc_start: 0.8704 (tp) cc_final: 0.8348 (tp) REVERT: D 250 GLU cc_start: 0.7774 (tp30) cc_final: 0.7464 (tt0) REVERT: D 269 GLN cc_start: 0.7655 (mt0) cc_final: 0.7416 (mt0) REVERT: F 159 ASP cc_start: 0.7662 (m-30) cc_final: 0.7281 (m-30) REVERT: F 231 ARG cc_start: 0.7703 (mtm180) cc_final: 0.7486 (mtm180) REVERT: F 255 SER cc_start: 0.8969 (OUTLIER) cc_final: 0.8340 (m) REVERT: G 113 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7993 (mt) REVERT: G 119 LYS cc_start: 0.6590 (tptp) cc_final: 0.6219 (tppt) REVERT: G 123 SER cc_start: 0.7447 (OUTLIER) cc_final: 0.7174 (m) REVERT: G 231 ARG cc_start: 0.7534 (ttm110) cc_final: 0.7124 (ttp80) REVERT: H 107 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8003 (ttpt) REVERT: H 147 ASP cc_start: 0.7250 (p0) cc_final: 0.6975 (p0) REVERT: H 163 ASP cc_start: 0.8043 (m-30) cc_final: 0.7658 (m-30) REVERT: H 203 ASP cc_start: 0.7937 (t0) cc_final: 0.7707 (t0) REVERT: H 264 ASP cc_start: 0.7133 (p0) cc_final: 0.6758 (p0) REVERT: h 582 TYR cc_start: 0.5583 (t80) cc_final: 0.5345 (t80) REVERT: I 238 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7857 (mt-10) REVERT: J 268 LEU cc_start: 0.8323 (tp) cc_final: 0.8014 (tp) REVERT: j 576 GLU cc_start: 0.8101 (tp30) cc_final: 0.7855 (tp30) outliers start: 47 outliers final: 29 residues processed: 351 average time/residue: 0.1970 time to fit residues: 103.2120 Evaluate side-chains 341 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 308 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS 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 156 ASP 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 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 113 LEU Chi-restraints excluded: chain G residue 123 SER 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 107 LYS Chi-restraints excluded: chain H residue 179 VAL 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 114 LYS Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 253 ILE 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: 3.9990 chunk 156 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 190 optimal weight: 0.0980 chunk 147 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 259 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.142127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.108398 restraints weight = 30269.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.109834 restraints weight = 32978.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.110357 restraints weight = 27747.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110612 restraints weight = 23115.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110941 restraints weight = 21824.888| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 23496 Z= 0.107 Angle : 0.516 8.803 31799 Z= 0.273 Chirality : 0.041 0.283 3531 Planarity : 0.004 0.035 3858 Dihedral : 15.435 177.554 3514 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.56 % Allowed : 13.51 % Favored : 84.93 % 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: 2.00 (0.16), residues: 2670 helix: 1.94 (0.13), residues: 1600 sheet: 2.16 (0.32), residues: 230 loop : -0.06 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 85 TYR 0.019 0.001 TYR a 575 PHE 0.010 0.001 PHE J 106 TRP 0.013 0.001 TRP G 20 HIS 0.002 0.000 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (23487) covalent geometry : angle 0.51612 / 0.27 (31799) hydrogen bonds : bond 0.03515 / 3.63 ( 1147) hydrogen bonds : angle 4.27315 / 4.04 ( 3285) Misc. bond : bond 0.00210 / 0.17 ( 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 369 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 332 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7598 (tttm) cc_final: 0.7183 (ttpt) REVERT: A 113 LEU cc_start: 0.8625 (mt) cc_final: 0.8080 (mt) REVERT: B 211 TRP cc_start: 0.8631 (OUTLIER) cc_final: 0.8417 (t-100) REVERT: B 235 SER cc_start: 0.8441 (m) cc_final: 0.8186 (t) REVERT: C 182 ARG cc_start: 0.7068 (ttm-80) cc_final: 0.6566 (ttp-110) REVERT: C 230 LEU cc_start: 0.8224 (mt) cc_final: 0.8019 (tp) REVERT: D 203 ASP cc_start: 0.7710 (t0) cc_final: 0.7339 (t0) REVERT: D 229 MET cc_start: 0.8192 (mmm) cc_final: 0.7937 (mmt) REVERT: D 230 LEU cc_start: 0.8645 (tp) cc_final: 0.8321 (tp) REVERT: D 269 GLN cc_start: 0.7682 (mt0) cc_final: 0.7434 (mt0) REVERT: F 159 ASP cc_start: 0.7655 (m-30) cc_final: 0.7286 (m-30) REVERT: F 231 ARG cc_start: 0.7695 (mtm180) cc_final: 0.7460 (mtm180) REVERT: F 255 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8326 (m) REVERT: F 261 LYS cc_start: 0.6710 (mmtt) cc_final: 0.6409 (mtpt) REVERT: G 113 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7786 (mt) REVERT: G 123 SER cc_start: 0.7375 (OUTLIER) cc_final: 0.7108 (m) REVERT: G 231 ARG cc_start: 0.7542 (ttm110) cc_final: 0.7074 (ttp80) REVERT: G 269 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7747 (tp-100) REVERT: H 107 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7976 (ttpt) REVERT: H 163 ASP cc_start: 0.8061 (m-30) cc_final: 0.7690 (m-30) REVERT: H 203 ASP cc_start: 0.7966 (t0) cc_final: 0.7721 (t0) REVERT: H 264 ASP cc_start: 0.7195 (p0) cc_final: 0.6805 (p0) REVERT: h 577 GLN cc_start: 0.7503 (tm-30) cc_final: 0.6222 (tm-30) REVERT: I 231 ARG cc_start: 0.7180 (ttm110) cc_final: 0.6893 (ttp-110) REVERT: I 238 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7872 (mt-10) REVERT: J 106 PHE cc_start: 0.8221 (m-80) cc_final: 0.8010 (m-80) outliers start: 37 outliers final: 23 residues processed: 355 average time/residue: 0.1908 time to fit residues: 101.7186 Evaluate side-chains 339 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 311 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 260 LEU 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 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 180 ILE 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 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 107 LYS 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 175 ARG Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 253 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 225 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 206 ASN J 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103293 restraints weight = 30298.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104865 restraints weight = 32210.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105434 restraints weight = 25682.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.105625 restraints weight = 22291.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.105681 restraints weight = 21242.412| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 23496 Z= 0.239 Angle : 0.661 7.546 31799 Z= 0.340 Chirality : 0.046 0.280 3531 Planarity : 0.005 0.036 3858 Dihedral : 15.616 179.970 3514 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.28 % Allowed : 13.76 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.16), residues: 2670 helix: 1.53 (0.13), residues: 1620 sheet: 1.68 (0.28), residues: 280 loop : -0.41 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 579 TYR 0.028 0.002 TYR a 575 PHE 0.014 0.002 PHE D 106 TRP 0.012 0.002 TRP G 20 HIS 0.007 0.002 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.24 (23487) covalent geometry : angle 0.66071 / 0.34 (31799) hydrogen bonds : bond 0.05192 / 5.29 ( 1147) hydrogen bonds : angle 4.47808 / 4.32 ( 3285) Misc. bond : bond 0.00441 / 0.36 ( 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 374 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 320 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7711 (tttm) cc_final: 0.7205 (ttpt) REVERT: A 205 LYS cc_start: 0.8514 (tmtt) cc_final: 0.8047 (tptp) REVERT: B 235 SER cc_start: 0.8435 (m) cc_final: 0.8218 (t) REVERT: C 182 ARG cc_start: 0.7261 (ttm-80) cc_final: 0.6718 (ttp-110) REVERT: C 230 LEU cc_start: 0.8325 (mt) cc_final: 0.8019 (tp) REVERT: D 203 ASP cc_start: 0.7915 (t0) cc_final: 0.7564 (t0) REVERT: E 159 ASP cc_start: 0.7767 (m-30) cc_final: 0.7063 (m-30) REVERT: E 181 LYS cc_start: 0.8251 (mttt) cc_final: 0.7771 (mtmt) REVERT: E 214 MET cc_start: 0.6918 (mtp) cc_final: 0.6416 (ttm) REVERT: F 159 ASP cc_start: 0.7693 (m-30) cc_final: 0.7248 (m-30) REVERT: F 255 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8190 (m) REVERT: F 264 ASP cc_start: 0.7015 (p0) cc_final: 0.6532 (t0) REVERT: G 113 LEU cc_start: 0.8404 (mt) cc_final: 0.8051 (mt) REVERT: G 119 LYS cc_start: 0.6696 (tptp) cc_final: 0.6216 (tptm) REVERT: G 123 SER cc_start: 0.7616 (OUTLIER) cc_final: 0.7326 (m) REVERT: G 231 ARG cc_start: 0.7573 (ttm110) cc_final: 0.7046 (ttp80) REVERT: H 147 ASP cc_start: 0.7332 (p0) cc_final: 0.7079 (p0) REVERT: H 163 ASP cc_start: 0.8078 (m-30) cc_final: 0.7642 (m-30) REVERT: H 264 ASP cc_start: 0.7319 (p0) cc_final: 0.6983 (p0) REVERT: I 78 LYS cc_start: 0.7722 (mttt) cc_final: 0.7283 (mttm) REVERT: I 238 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7858 (mt-10) REVERT: I 264 ASP cc_start: 0.5821 (p0) cc_final: 0.5374 (p0) REVERT: i 580 GLU cc_start: 0.6620 (tm-30) cc_final: 0.6413 (tm-30) REVERT: J 64 THR cc_start: 0.8705 (p) cc_final: 0.8337 (p) outliers start: 54 outliers final: 39 residues processed: 356 average time/residue: 0.2007 time to fit residues: 105.4443 Evaluate side-chains 340 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 299 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain B residue 20 TRP 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 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 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 255 SER Chi-restraints excluded: chain F residue 257 SER 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 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 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 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 113 LEU Chi-restraints excluded: chain J residue 175 ARG Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 268 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 195 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 258 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 ASN G 98 GLN I 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.105546 restraints weight = 29922.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107035 restraints weight = 32302.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107666 restraints weight = 24542.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107886 restraints weight = 22676.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.108197 restraints weight = 20533.090| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23496 Z= 0.118 Angle : 0.547 8.920 31799 Z= 0.288 Chirality : 0.041 0.290 3531 Planarity : 0.004 0.054 3858 Dihedral : 15.500 178.846 3514 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.60 % Allowed : 14.73 % Favored : 83.66 % 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: 1.80 (0.16), residues: 2670 helix: 1.80 (0.13), residues: 1620 sheet: 1.75 (0.28), residues: 280 loop : -0.27 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 579 TYR 0.016 0.001 TYR a 575 PHE 0.006 0.001 PHE H 190 TRP 0.015 0.001 TRP C 45 HIS 0.004 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (23487) covalent geometry : angle 0.54708 / 0.29 (31799) hydrogen bonds : bond 0.03874 / 3.97 ( 1147) hydrogen bonds : angle 4.30451 / 4.10 ( 3285) Misc. bond : bond 0.00252 / 0.21 ( 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 360 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 322 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6664 (tt) REVERT: A 107 LYS cc_start: 0.7693 (tttm) cc_final: 0.7195 (ttpt) REVERT: A 113 LEU cc_start: 0.8695 (mt) cc_final: 0.8188 (mt) REVERT: A 205 LYS cc_start: 0.8542 (tmtt) cc_final: 0.8016 (tptp) REVERT: A 238 GLU cc_start: 0.8386 (pm20) cc_final: 0.7851 (pm20) REVERT: C 182 ARG cc_start: 0.7260 (ttm-80) cc_final: 0.6698 (ttp-110) REVERT: C 230 LEU cc_start: 0.8262 (mt) cc_final: 0.7982 (tp) REVERT: D 203 ASP cc_start: 0.7874 (t0) cc_final: 0.7536 (t0) REVERT: E 47 ASP cc_start: 0.8049 (t0) cc_final: 0.7841 (m-30) REVERT: E 159 ASP cc_start: 0.7643 (m-30) cc_final: 0.6985 (m-30) REVERT: E 181 LYS cc_start: 0.8206 (mttt) cc_final: 0.7761 (mtmt) REVERT: E 214 MET cc_start: 0.6831 (mtp) cc_final: 0.6384 (ttm) REVERT: F 159 ASP cc_start: 0.7668 (m-30) cc_final: 0.7214 (m-30) REVERT: F 255 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8321 (m) REVERT: F 264 ASP cc_start: 0.6952 (p0) cc_final: 0.6501 (t0) REVERT: G 113 LEU cc_start: 0.8269 (mt) cc_final: 0.7927 (mt) REVERT: G 119 LYS cc_start: 0.6832 (tptp) cc_final: 0.6176 (tptm) REVERT: G 213 GLN cc_start: 0.7380 (tm-30) cc_final: 0.7117 (tm-30) REVERT: G 231 ARG cc_start: 0.7549 (ttm110) cc_final: 0.7078 (ttp80) REVERT: H 163 ASP cc_start: 0.8084 (m-30) cc_final: 0.7620 (m-30) REVERT: I 231 ARG cc_start: 0.7176 (ttm110) cc_final: 0.6887 (ttp-110) REVERT: I 238 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7837 (mt-10) REVERT: J 64 THR cc_start: 0.8761 (p) cc_final: 0.8431 (p) REVERT: J 160 ILE cc_start: 0.8771 (mt) cc_final: 0.8283 (mm) outliers start: 38 outliers final: 26 residues processed: 349 average time/residue: 0.1913 time to fit residues: 100.4128 Evaluate side-chains 333 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 305 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 D residue 229 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 ILE 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 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 Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 268 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 103 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 247 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 ASN F 206 ASN H 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.104591 restraints weight = 30172.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105900 restraints weight = 31762.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.106840 restraints weight = 25851.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.106999 restraints weight = 22248.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107103 restraints weight = 20987.493| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23496 Z= 0.156 Angle : 0.574 8.535 31799 Z= 0.300 Chirality : 0.042 0.280 3531 Planarity : 0.004 0.036 3858 Dihedral : 15.570 179.648 3514 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.60 % Allowed : 14.86 % 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: 1.76 (0.13), residues: 1620 sheet: 1.68 (0.28), residues: 280 loop : -0.33 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG d 579 TYR 0.018 0.001 TYR a 575 PHE 0.008 0.001 PHE C 125 TRP 0.013 0.001 TRP G 20 HIS 0.006 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (23487) covalent geometry : angle 0.57372 / 0.30 (31799) hydrogen bonds : bond 0.04189 / 4.28 ( 1147) hydrogen bonds : angle 4.33722 / 4.16 ( 3285) Misc. bond : bond 0.00335 / 0.28 ( 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 352 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 314 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6694 (tt) REVERT: A 107 LYS cc_start: 0.7738 (tttm) cc_final: 0.7247 (ttpt) REVERT: A 113 LEU cc_start: 0.8640 (mt) cc_final: 0.8142 (mt) REVERT: A 205 LYS cc_start: 0.8541 (tmtt) cc_final: 0.8042 (tptp) REVERT: A 206 ASN cc_start: 0.8504 (m-40) cc_final: 0.8093 (m110) REVERT: A 238 GLU cc_start: 0.8486 (pm20) cc_final: 0.8102 (pm20) REVERT: C 182 ARG cc_start: 0.7305 (ttm-80) cc_final: 0.6720 (ttp-110) REVERT: C 230 LEU cc_start: 0.8272 (mt) cc_final: 0.7983 (tp) REVERT: D 203 ASP cc_start: 0.7925 (t0) cc_final: 0.7600 (t0) REVERT: E 47 ASP cc_start: 0.8072 (t0) cc_final: 0.7858 (m-30) REVERT: E 159 ASP cc_start: 0.7764 (m-30) cc_final: 0.7010 (m-30) REVERT: E 181 LYS cc_start: 0.8222 (mttt) cc_final: 0.7757 (mtmt) REVERT: E 214 MET cc_start: 0.6957 (mtp) cc_final: 0.6606 (ttm) REVERT: E 229 MET cc_start: 0.7668 (mmt) cc_final: 0.7385 (mtt) REVERT: F 159 ASP cc_start: 0.7693 (m-30) cc_final: 0.7353 (m-30) REVERT: F 264 ASP cc_start: 0.7026 (p0) cc_final: 0.6719 (t0) REVERT: G 113 LEU cc_start: 0.8254 (mt) cc_final: 0.7925 (mt) REVERT: G 119 LYS cc_start: 0.6789 (tptp) cc_final: 0.6045 (tptm) REVERT: G 213 GLN cc_start: 0.7343 (tm-30) cc_final: 0.7084 (tm-30) REVERT: G 231 ARG cc_start: 0.7571 (ttm110) cc_final: 0.7029 (ttp80) REVERT: H 163 ASP cc_start: 0.8102 (m-30) cc_final: 0.7706 (m-30) REVERT: H 213 GLN cc_start: 0.7887 (tt0) cc_final: 0.7638 (tt0) REVERT: H 231 ARG cc_start: 0.7759 (ttm170) cc_final: 0.7419 (tpp80) REVERT: H 264 ASP cc_start: 0.7386 (p0) cc_final: 0.7099 (p0) REVERT: I 231 ARG cc_start: 0.7208 (ttm110) cc_final: 0.6829 (mtm-85) REVERT: I 238 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7827 (mt-10) REVERT: J 20 TRP cc_start: 0.7113 (t60) cc_final: 0.6806 (t60) REVERT: J 64 THR cc_start: 0.8745 (p) cc_final: 0.8377 (p) REVERT: J 160 ILE cc_start: 0.8767 (mt) cc_final: 0.8271 (mm) outliers start: 38 outliers final: 29 residues processed: 342 average time/residue: 0.1920 time to fit residues: 98.7905 Evaluate side-chains 337 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 307 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 255 SER 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 D residue 229 MET Chi-restraints excluded: chain D residue 256 LEU 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 153 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 I residue 255 SER Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 43 optimal weight: 0.8980 chunk 196 optimal weight: 0.0970 chunk 230 optimal weight: 0.0870 chunk 128 optimal weight: 0.8980 chunk 144 optimal weight: 0.0470 chunk 193 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107540 restraints weight = 30039.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.107989 restraints weight = 33107.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108777 restraints weight = 29748.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109284 restraints weight = 23845.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109430 restraints weight = 22216.437| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23496 Z= 0.101 Angle : 0.516 8.246 31799 Z= 0.276 Chirality : 0.040 0.284 3531 Planarity : 0.004 0.039 3858 Dihedral : 15.485 179.876 3514 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.76 % Allowed : 15.87 % Favored : 83.37 % 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: 1.98 (0.16), residues: 2670 helix: 1.93 (0.13), residues: 1620 sheet: 1.76 (0.27), residues: 280 loop : -0.16 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 579 TYR 0.011 0.001 TYR a 575 PHE 0.007 0.001 PHE A 106 TRP 0.019 0.002 TRP G 45 HIS 0.002 0.000 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.10 (23487) covalent geometry : angle 0.51650 / 0.28 (31799) hydrogen bonds : bond 0.03289 / 3.37 ( 1147) hydrogen bonds : angle 4.26373 / 4.05 ( 3285) Misc. bond : bond 0.00181 / 0.15 ( 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 352 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 334 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6644 (tt) REVERT: A 107 LYS cc_start: 0.7741 (tttm) cc_final: 0.7165 (ttpt) REVERT: A 113 LEU cc_start: 0.8575 (mt) cc_final: 0.8103 (mt) REVERT: A 205 LYS cc_start: 0.8582 (tmtt) cc_final: 0.8031 (tptp) REVERT: A 206 ASN cc_start: 0.8485 (m-40) cc_final: 0.8140 (m110) REVERT: A 238 GLU cc_start: 0.8474 (pm20) cc_final: 0.8237 (pm20) REVERT: C 182 ARG cc_start: 0.7299 (ttm-80) cc_final: 0.6706 (ttp-110) REVERT: C 230 LEU cc_start: 0.8233 (mt) cc_final: 0.8001 (tp) REVERT: D 203 ASP cc_start: 0.7879 (t0) cc_final: 0.7585 (t0) REVERT: E 159 ASP cc_start: 0.7621 (m-30) cc_final: 0.6913 (m-30) REVERT: E 181 LYS cc_start: 0.8125 (mttt) cc_final: 0.7682 (mtmt) REVERT: E 214 MET cc_start: 0.6900 (mtp) cc_final: 0.6623 (ttm) REVERT: E 229 MET cc_start: 0.7678 (mmt) cc_final: 0.7366 (mtt) REVERT: F 159 ASP cc_start: 0.7652 (m-30) cc_final: 0.7175 (m-30) REVERT: G 62 SER cc_start: 0.8338 (t) cc_final: 0.8042 (m) REVERT: G 113 LEU cc_start: 0.8339 (mt) cc_final: 0.8032 (mt) REVERT: G 119 LYS cc_start: 0.6781 (tptp) cc_final: 0.6066 (tptm) REVERT: G 231 ARG cc_start: 0.7499 (ttm110) cc_final: 0.7029 (ttp80) REVERT: H 163 ASP cc_start: 0.8110 (m-30) cc_final: 0.7675 (m-30) REVERT: H 264 ASP cc_start: 0.7427 (p0) cc_final: 0.7051 (p0) REVERT: I 231 ARG cc_start: 0.7259 (ttm110) cc_final: 0.6915 (mtm-85) REVERT: I 238 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7871 (mt-10) REVERT: J 20 TRP cc_start: 0.7102 (t60) cc_final: 0.6797 (t60) REVERT: J 85 ARG cc_start: 0.6575 (mmt90) cc_final: 0.5806 (mtp180) REVERT: J 140 MET cc_start: 0.9203 (ttp) cc_final: 0.8901 (ttm) REVERT: J 160 ILE cc_start: 0.8693 (mt) cc_final: 0.8244 (mm) outliers start: 18 outliers final: 14 residues processed: 347 average time/residue: 0.1919 time to fit residues: 100.1309 Evaluate side-chains 332 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 317 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 156 ASP Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 117 VAL 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 H residue 21 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 96 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 144 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.6722 > 50:) chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 209 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 182 optimal weight: 0.4980 chunk 180 optimal weight: 0.4980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107562 restraints weight = 30049.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108854 restraints weight = 32329.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109633 restraints weight = 25861.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110117 restraints weight = 22411.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.110361 restraints weight = 21089.799| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23496 Z= 0.107 Angle : 0.524 8.704 31799 Z= 0.278 Chirality : 0.041 0.279 3531 Planarity : 0.004 0.037 3858 Dihedral : 15.505 178.867 3514 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.89 % Allowed : 16.04 % Favored : 83.07 % 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: 2.06 (0.16), residues: 2670 helix: 1.99 (0.13), residues: 1620 sheet: 1.73 (0.27), residues: 280 loop : -0.06 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG d 579 TYR 0.016 0.001 TYR d 575 PHE 0.005 0.001 PHE C 106 TRP 0.018 0.001 TRP C 45 HIS 0.003 0.000 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (23487) covalent geometry : angle 0.52448 / 0.28 (31799) hydrogen bonds : bond 0.03314 / 3.38 ( 1147) hydrogen bonds : angle 4.25041 / 4.05 ( 3285) Misc. bond : bond 0.00222 / 0.18 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3672.96 seconds wall clock time: 64 minutes 42.83 seconds (3882.83 seconds total)