Starting phenix.real_space_refine on Sun Aug 24 21:06:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7svv_25454/08_2025/7svv_25454.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svv_25454/08_2025/7svv_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_25454/08_2025/7svv_25454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svv_25454/08_2025/7svv_25454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7svv_25454/08_2025/7svv_25454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svv_25454/08_2025/7svv_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-2.0-5787/lib/python3.9/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: 5.03, per 1000 atoms: 0.22 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: 2.08 Conformation dependent library (CDL) restraints added in 821.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.18 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: 2.87 Time building geometry restraints manager: 2.71 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: 14010 34.93 - 69.85: 494 69.85 - 104.78: 75 104.78 - 139.71: 3 139.71 - 174.63: 10 Dihedral angle restraints: 14592 sinusoidal: 6732 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 14589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 3065 0.131 - 0.262: 409 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: 1.030 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.950 Find NCS groups from input model: 0.350 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.024 0.869 23496 Z= 1.976 Angle : 1.877 26.945 31799 Z= 1.297 Chirality : 0.100 0.656 3531 Planarity : 0.010 0.059 3858 Dihedral : 16.778 174.635 9512 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 aren 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 covalent geometry : bond 0.02033 (23487) covalent geometry : angle 1.87664 (31799) hydrogen bonds : bond 0.24473 ( 1147) hydrogen bonds : angle 7.91435 ( 3285) Misc. bond : bond 0.69749 ( 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 : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7512 (ttm110) REVERT: B 40 LYS cc_start: 0.8168 (tptp) cc_final: 0.7947 (ttmt) REVERT: B 47 ASP cc_start: 0.7479 (t70) cc_final: 0.7186 (t0) REVERT: B 54 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7566 (tttp) REVERT: B 188 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7878 (mm-30) REVERT: B 230 LEU cc_start: 0.8705 (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: 0.7494 (t) REVERT: F 47 ASP cc_start: 0.7945 (t70) cc_final: 0.7608 (t0) REVERT: F 54 LYS cc_start: 0.8306 (mmtm) cc_final: 0.7991 (tttm) REVERT: F 140 MET cc_start: 0.9285 (ttm) cc_final: 0.9047 (ttp) REVERT: F 159 ASP cc_start: 0.6987 (m-30) cc_final: 0.6532 (m-30) REVERT: F 163 ASP cc_start: 0.8125 (m-30) cc_final: 0.7855 (m-30) REVERT: F 229 MET cc_start: 0.8570 (mmm) cc_final: 0.8234 (mmm) REVERT: G 27 ARG cc_start: 0.7204 (ttp80) cc_final: 0.6763 (ptt90) REVERT: G 119 LYS cc_start: 0.6347 (tptp) cc_final: 0.6093 (tppt) REVERT: G 139 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8102 (mt-10) REVERT: G 162 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6053 (mm-30) REVERT: G 231 ARG cc_start: 0.7312 (ttm110) cc_final: 0.7110 (ttp80) REVERT: H 107 LYS cc_start: 0.8113 (tttm) cc_final: 0.7723 (mtmt) REVERT: H 140 MET cc_start: 0.9377 (ttm) cc_final: 0.9137 (ttm) REVERT: H 163 ASP cc_start: 0.7745 (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: 0.2028 time to fit residues: 201.2487 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 : 0.652 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 223 ASN I 37 GLN I 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.114300 restraints weight = 30501.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115446 restraints weight = 32597.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116636 restraints weight = 26438.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116635 restraints weight = 22626.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116799 restraints weight = 21930.222| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23496 Z= 0.142 Angle : 0.585 7.032 31799 Z= 0.312 Chirality : 0.042 0.239 3531 Planarity : 0.005 0.038 3858 Dihedral : 17.243 179.903 3794 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.69 % Allowed : 8.70 % Favored : 89.62 % 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 aren not related in a simple way. whole: 1.63 (0.16), residues: 2670 helix: 1.44 (0.13), residues: 1600 sheet: 2.60 (0.31), residues: 230 loop : 0.06 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 191 TYR 0.013 0.001 TYR j 575 PHE 0.008 0.001 PHE F 196 TRP 0.009 0.001 TRP J 45 HIS 0.004 0.001 HIS I 97 Details of bonding type rmsd covalent geometry : bond 0.00305 (23487) covalent geometry : angle 0.58521 (31799) hydrogen bonds : bond 0.04210 ( 1147) hydrogen bonds : angle 4.60346 ( 3285) Misc. bond : bond 0.00343 ( 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 445 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 405 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7427 (tttm) cc_final: 0.6898 (ttpt) REVERT: A 113 LEU cc_start: 0.8591 (mt) cc_final: 0.8204 (mt) REVERT: A 127 ASP cc_start: 0.7001 (m-30) cc_final: 0.6691 (m-30) REVERT: A 203 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7832 (t0) REVERT: A 205 LYS cc_start: 0.8233 (tmmt) cc_final: 0.8005 (tptp) REVERT: B 211 TRP cc_start: 0.8541 (t-100) cc_final: 0.8256 (t-100) REVERT: B 230 LEU cc_start: 0.8863 (mt) cc_final: 0.8538 (tp) REVERT: B 265 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7614 (mmtt) REVERT: B 268 LEU cc_start: 0.8881 (tp) cc_final: 0.8674 (tt) REVERT: b 571 GLU cc_start: 0.6836 (pm20) cc_final: 0.6635 (pm20) REVERT: C 182 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.6646 (ttp-110) REVERT: C 230 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7948 (tp) REVERT: D 113 LEU cc_start: 0.8426 (mt) cc_final: 0.8211 (mt) REVERT: D 203 ASP cc_start: 0.7654 (t0) cc_final: 0.7294 (t0) REVERT: D 229 MET cc_start: 0.8149 (mmm) cc_final: 0.7858 (mmt) REVERT: D 230 LEU cc_start: 0.8667 (mt) cc_final: 0.8314 (tp) REVERT: D 250 GLU cc_start: 0.7900 (tp30) cc_final: 0.7521 (tt0) REVERT: E 181 LYS cc_start: 0.8207 (mttt) cc_final: 0.7847 (mtmt) REVERT: E 210 MET cc_start: 0.8135 (ttm) cc_final: 0.7930 (ttm) REVERT: F 140 MET cc_start: 0.9076 (ttm) cc_final: 0.8866 (ttt) REVERT: F 159 ASP cc_start: 0.7617 (m-30) cc_final: 0.7066 (m-30) REVERT: G 33 ILE cc_start: 0.9012 (mt) cc_final: 0.8807 (mm) REVERT: G 76 ARG cc_start: 0.7437 (mtp180) cc_final: 0.6916 (mtp180) REVERT: G 113 LEU cc_start: 0.7781 (mt) cc_final: 0.7453 (mt) REVERT: G 119 LYS cc_start: 0.6374 (tptp) cc_final: 0.6142 (tppt) REVERT: G 159 ASP cc_start: 0.7802 (m-30) cc_final: 0.7538 (m-30) REVERT: G 162 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6396 (mm-30) REVERT: G 231 ARG cc_start: 0.7172 (ttm110) cc_final: 0.6846 (ttp80) REVERT: H 159 ASP cc_start: 0.7413 (m-30) cc_final: 0.6902 (m-30) REVERT: H 163 ASP cc_start: 0.8013 (m-30) cc_final: 0.7734 (m-30) REVERT: H 203 ASP cc_start: 0.7900 (t0) cc_final: 0.7614 (t0) REVERT: I 206 ASN cc_start: 0.7827 (m-40) cc_final: 0.7612 (m-40) REVERT: I 238 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7826 (mt-10) REVERT: J 78 LYS cc_start: 0.7950 (mttt) cc_final: 0.7554 (mtmt) REVERT: J 223 ASN cc_start: 0.6605 (m-40) cc_final: 0.6337 (t0) REVERT: J 269 GLN cc_start: 0.7621 (mt0) cc_final: 0.7307 (mt0) outliers start: 40 outliers final: 20 residues processed: 425 average time/residue: 0.1640 time to fit residues: 101.8260 Evaluate side-chains 334 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 311 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 256 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 62 SER 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 G residue 187 LEU Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain I residue 64 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 0.0060 chunk 201 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 51 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 199 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 206 ASN I 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.146066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112866 restraints weight = 30409.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114159 restraints weight = 32117.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115432 restraints weight = 26177.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115486 restraints weight = 21803.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115647 restraints weight = 21160.420| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23496 Z= 0.096 Angle : 0.482 6.241 31799 Z= 0.257 Chirality : 0.039 0.211 3531 Planarity : 0.004 0.035 3858 Dihedral : 16.353 176.633 3794 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.06 % Allowed : 11.02 % Favored : 87.93 % 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 aren not related in a simple way. whole: 2.25 (0.16), residues: 2670 helix: 2.02 (0.13), residues: 1600 sheet: 2.25 (0.29), residues: 280 loop : 0.18 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG j 579 TYR 0.009 0.001 TYR a 575 PHE 0.007 0.001 PHE C 106 TRP 0.013 0.001 TRP I 45 HIS 0.003 0.000 HIS J 77 Details of bonding type rmsd covalent geometry : bond 0.00197 (23487) covalent geometry : angle 0.48233 (31799) hydrogen bonds : bond 0.03077 ( 1147) hydrogen bonds : angle 4.27771 ( 3285) Misc. bond : bond 0.00222 ( 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 390 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 365 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7433 (tttm) cc_final: 0.7112 (ttpt) REVERT: A 113 LEU cc_start: 0.8404 (mt) cc_final: 0.7901 (mt) REVERT: A 203 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7764 (t0) REVERT: A 205 LYS cc_start: 0.8276 (tmmt) cc_final: 0.8005 (tptp) REVERT: B 211 TRP cc_start: 0.8558 (t-100) cc_final: 0.8304 (t-100) REVERT: B 230 LEU cc_start: 0.8706 (mt) cc_final: 0.8431 (tp) REVERT: C 182 ARG cc_start: 0.7219 (ttm-80) cc_final: 0.6669 (ttp-110) REVERT: C 230 LEU cc_start: 0.8185 (mt) cc_final: 0.7962 (tp) REVERT: D 113 LEU cc_start: 0.8215 (mt) cc_final: 0.7912 (mt) REVERT: D 203 ASP cc_start: 0.7927 (t0) cc_final: 0.7538 (t0) REVERT: D 229 MET cc_start: 0.8196 (mmm) cc_final: 0.7893 (mmt) REVERT: D 230 LEU cc_start: 0.8576 (mt) cc_final: 0.8291 (tp) REVERT: D 250 GLU cc_start: 0.7842 (tp30) cc_final: 0.7517 (mt-10) REVERT: E 181 LYS cc_start: 0.8099 (mttt) cc_final: 0.7753 (mtmt) REVERT: F 159 ASP cc_start: 0.7520 (m-30) cc_final: 0.6950 (m-30) REVERT: F 191 ARG cc_start: 0.8175 (ttt90) cc_final: 0.7961 (ttt90) REVERT: F 255 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8327 (m) REVERT: F 264 ASP cc_start: 0.6978 (p0) cc_final: 0.6629 (t0) REVERT: G 162 GLU cc_start: 0.6296 (mt-10) cc_final: 0.6033 (mm-30) REVERT: G 231 ARG cc_start: 0.7277 (ttm110) cc_final: 0.6924 (ttp80) REVERT: G 255 SER cc_start: 0.7617 (OUTLIER) cc_final: 0.7392 (m) REVERT: G 269 GLN cc_start: 0.7840 (tp-100) cc_final: 0.7582 (tp-100) REVERT: H 131 GLU cc_start: 0.6397 (tp30) cc_final: 0.6192 (tp30) REVERT: H 163 ASP cc_start: 0.8035 (m-30) cc_final: 0.7690 (m-30) REVERT: H 203 ASP cc_start: 0.7956 (t0) cc_final: 0.7707 (t0) REVERT: I 206 ASN cc_start: 0.7857 (m-40) cc_final: 0.7580 (m-40) REVERT: I 223 ASN cc_start: 0.6581 (m110) cc_final: 0.5918 (t0) REVERT: I 238 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7764 (mt-10) REVERT: J 223 ASN cc_start: 0.6739 (m-40) cc_final: 0.6396 (t0) REVERT: J 269 GLN cc_start: 0.7647 (mt0) cc_final: 0.7368 (mt0) outliers start: 25 outliers final: 11 residues processed: 378 average time/residue: 0.2045 time to fit residues: 113.0908 Evaluate side-chains 318 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 304 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 64 THR 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 E residue 235 SER 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 255 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 81 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 69 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 260 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 223 ASN D 269 GLN H 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103657 restraints weight = 30277.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106144 restraints weight = 32183.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106690 restraints weight = 24413.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106751 restraints weight = 20845.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.106835 restraints weight = 20275.297| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.004 0.039 23496 Z= 0.176 Angle : 0.585 6.351 31799 Z= 0.307 Chirality : 0.043 0.226 3531 Planarity : 0.004 0.037 3858 Dihedral : 16.562 179.592 3794 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.94 % Allowed : 12.58 % Favored : 85.48 % 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 aren not related in a simple way. whole: 1.93 (0.16), residues: 2670 helix: 1.83 (0.13), residues: 1580 sheet: 2.00 (0.27), residues: 280 loop : -0.02 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 579 TYR 0.014 0.001 TYR a 575 PHE 0.012 0.002 PHE J 106 TRP 0.012 0.002 TRP F 20 HIS 0.006 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00414 (23487) covalent geometry : angle 0.58549 (31799) hydrogen bonds : bond 0.04656 ( 1147) hydrogen bonds : angle 4.41463 ( 3285) Misc. bond : bond 0.00358 ( 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 388 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 342 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7872 (tttm) cc_final: 0.7285 (ttpt) REVERT: A 205 LYS cc_start: 0.8429 (tmmt) cc_final: 0.8184 (tptp) REVERT: B 230 LEU cc_start: 0.8743 (mt) cc_final: 0.8511 (tp) REVERT: C 182 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.6720 (ttp-110) REVERT: C 230 LEU cc_start: 0.8263 (mt) cc_final: 0.7768 (tp) REVERT: D 113 LEU cc_start: 0.8452 (mt) cc_final: 0.8130 (mt) REVERT: D 203 ASP cc_start: 0.7978 (t0) cc_final: 0.7647 (t0) REVERT: D 250 GLU cc_start: 0.8027 (tp30) cc_final: 0.7727 (tt0) REVERT: E 159 ASP cc_start: 0.7968 (m-30) cc_final: 0.7142 (m-30) REVERT: E 181 LYS cc_start: 0.8277 (mttt) cc_final: 0.7800 (mtmt) REVERT: E 229 MET cc_start: 0.7757 (mmt) cc_final: 0.7531 (mtt) REVERT: F 159 ASP cc_start: 0.7551 (m-30) cc_final: 0.7201 (m-30) REVERT: F 229 MET cc_start: 0.8550 (mmm) cc_final: 0.7888 (mmt) REVERT: F 231 ARG cc_start: 0.7602 (mtm180) cc_final: 0.7347 (mtm180) REVERT: F 255 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8154 (m) REVERT: F 264 ASP cc_start: 0.7303 (p0) cc_final: 0.7013 (t0) REVERT: G 62 SER cc_start: 0.7893 (t) cc_final: 0.7602 (m) REVERT: G 119 LYS cc_start: 0.6784 (tptp) cc_final: 0.6048 (tptm) REVERT: G 231 ARG cc_start: 0.7552 (ttm110) cc_final: 0.7061 (ttp80) REVERT: H 163 ASP cc_start: 0.8113 (m-30) cc_final: 0.7637 (m-30) REVERT: h 577 GLN cc_start: 0.6842 (tt0) cc_final: 0.6340 (tm-30) REVERT: h 581 GLU cc_start: 0.5836 (mt-10) cc_final: 0.5099 (mt-10) REVERT: I 206 ASN cc_start: 0.8248 (m-40) cc_final: 0.7851 (m-40) REVERT: I 213 GLN cc_start: 0.8021 (tp40) cc_final: 0.7802 (mm-40) REVERT: I 238 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7827 (mt-10) REVERT: J 160 ILE cc_start: 0.8780 (mt) cc_final: 0.8327 (mm) REVERT: j 574 ASP cc_start: 0.8110 (t0) cc_final: 0.7831 (t0) outliers start: 46 outliers final: 30 residues processed: 374 average time/residue: 0.2049 time to fit residues: 112.2934 Evaluate side-chains 335 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 153 THR 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 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 153 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain h residue 572 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN D 269 GLN F 206 ASN H 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105827 restraints weight = 30107.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.106826 restraints weight = 32488.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107888 restraints weight = 27302.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108056 restraints weight = 23166.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108158 restraints weight = 21864.663| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23496 Z= 0.135 Angle : 0.518 6.601 31799 Z= 0.275 Chirality : 0.041 0.213 3531 Planarity : 0.004 0.036 3858 Dihedral : 16.419 179.403 3794 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.82 % Allowed : 13.34 % Favored : 84.85 % 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 aren not related in a simple way. whole: 1.91 (0.16), residues: 2670 helix: 1.82 (0.13), residues: 1610 sheet: 1.87 (0.27), residues: 280 loop : -0.08 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 579 TYR 0.010 0.001 TYR a 575 PHE 0.008 0.001 PHE C 125 TRP 0.014 0.001 TRP C 45 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00313 (23487) covalent geometry : angle 0.51826 (31799) hydrogen bonds : bond 0.03789 ( 1147) hydrogen bonds : angle 4.32831 ( 3285) Misc. bond : bond 0.00286 ( 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: 43 poor density : 327 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7922 (tttm) cc_final: 0.7370 (ttpt) REVERT: A 113 LEU cc_start: 0.8667 (mt) cc_final: 0.8191 (mt) REVERT: A 205 LYS cc_start: 0.8433 (tmmt) cc_final: 0.8195 (tptp) REVERT: A 206 ASN cc_start: 0.8394 (m-40) cc_final: 0.8167 (m110) REVERT: B 230 LEU cc_start: 0.8656 (mt) cc_final: 0.8402 (tp) REVERT: C 182 ARG cc_start: 0.7344 (ttm-80) cc_final: 0.6748 (ttp-110) REVERT: C 230 LEU cc_start: 0.8275 (mt) cc_final: 0.7983 (tp) REVERT: D 113 LEU cc_start: 0.8398 (mt) cc_final: 0.8134 (mt) REVERT: D 128 ARG cc_start: 0.7536 (tpt170) cc_final: 0.7153 (tpt170) REVERT: D 203 ASP cc_start: 0.7948 (t0) cc_final: 0.7541 (t0) REVERT: D 230 LEU cc_start: 0.8574 (mt) cc_final: 0.8286 (tp) REVERT: D 250 GLU cc_start: 0.7912 (tp30) cc_final: 0.7608 (tt0) REVERT: E 159 ASP cc_start: 0.7986 (m-30) cc_final: 0.7126 (m-30) REVERT: E 181 LYS cc_start: 0.8259 (mttt) cc_final: 0.7767 (mtmt) REVERT: F 159 ASP cc_start: 0.7669 (m-30) cc_final: 0.7228 (m-30) REVERT: F 231 ARG cc_start: 0.7593 (mtm180) cc_final: 0.7329 (mtm180) REVERT: F 264 ASP cc_start: 0.7085 (p0) cc_final: 0.6780 (t0) REVERT: G 62 SER cc_start: 0.8148 (t) cc_final: 0.7926 (m) REVERT: G 119 LYS cc_start: 0.6392 (tptp) cc_final: 0.5644 (tptm) REVERT: G 213 GLN cc_start: 0.7417 (tm-30) cc_final: 0.7199 (tm-30) REVERT: G 231 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7040 (ttp80) REVERT: H 163 ASP cc_start: 0.8141 (m-30) cc_final: 0.7631 (m-30) REVERT: I 206 ASN cc_start: 0.8262 (m-40) cc_final: 0.7833 (m-40) REVERT: I 223 ASN cc_start: 0.7085 (p0) cc_final: 0.6812 (m-40) REVERT: I 231 ARG cc_start: 0.7270 (ttm110) cc_final: 0.6820 (mtm-85) REVERT: I 238 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7863 (mt-10) REVERT: J 20 TRP cc_start: 0.7186 (t60) cc_final: 0.6938 (t60) REVERT: J 64 THR cc_start: 0.8773 (p) cc_final: 0.8414 (p) REVERT: J 81 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6423 (mt0) REVERT: J 160 ILE cc_start: 0.8777 (mt) cc_final: 0.8383 (mm) REVERT: j 574 ASP cc_start: 0.8071 (t0) cc_final: 0.7840 (t0) outliers start: 43 outliers final: 29 residues processed: 355 average time/residue: 0.1954 time to fit residues: 102.6720 Evaluate side-chains 334 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 304 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 235 SER 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 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 153 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 76 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 259 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN B 213 GLN D 269 GLN F 206 ASN H 223 ASN J 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107424 restraints weight = 29951.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109069 restraints weight = 30978.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109761 restraints weight = 24504.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110295 restraints weight = 21463.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110608 restraints weight = 20666.306| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23496 Z= 0.104 Angle : 0.481 8.088 31799 Z= 0.255 Chirality : 0.040 0.191 3531 Planarity : 0.003 0.035 3858 Dihedral : 16.246 178.725 3794 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.52 % Allowed : 13.89 % Favored : 84.59 % 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 aren not related in a simple way. whole: 2.11 (0.16), residues: 2670 helix: 1.99 (0.13), residues: 1610 sheet: 1.85 (0.27), residues: 280 loop : 0.03 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 579 TYR 0.007 0.001 TYR F 93 PHE 0.005 0.001 PHE C 125 TRP 0.015 0.001 TRP G 45 HIS 0.002 0.000 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00227 (23487) covalent geometry : angle 0.48125 (31799) hydrogen bonds : bond 0.03223 ( 1147) hydrogen bonds : angle 4.24463 ( 3285) Misc. bond : bond 0.00233 ( 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 374 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 338 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7789 (tttm) cc_final: 0.7244 (ttpt) REVERT: A 113 LEU cc_start: 0.8493 (mt) cc_final: 0.8059 (mt) REVERT: A 206 ASN cc_start: 0.8410 (m-40) cc_final: 0.8170 (m110) REVERT: B 230 LEU cc_start: 0.8701 (mt) cc_final: 0.8415 (tp) REVERT: C 180 ILE cc_start: 0.8518 (tt) cc_final: 0.8068 (tt) REVERT: C 182 ARG cc_start: 0.7357 (ttm-80) cc_final: 0.6741 (ttp-110) REVERT: C 230 LEU cc_start: 0.8295 (mt) cc_final: 0.8067 (tp) REVERT: D 113 LEU cc_start: 0.8192 (mt) cc_final: 0.7844 (mt) REVERT: D 123 SER cc_start: 0.7534 (p) cc_final: 0.7298 (m) REVERT: D 203 ASP cc_start: 0.7912 (t0) cc_final: 0.7635 (t0) REVERT: D 230 LEU cc_start: 0.8543 (mt) cc_final: 0.8299 (tp) REVERT: D 250 GLU cc_start: 0.7890 (tp30) cc_final: 0.7611 (tt0) REVERT: E 47 ASP cc_start: 0.7337 (m-30) cc_final: 0.7121 (m-30) REVERT: E 159 ASP cc_start: 0.7927 (m-30) cc_final: 0.7133 (m-30) REVERT: E 181 LYS cc_start: 0.8168 (mttt) cc_final: 0.7698 (mtmt) REVERT: F 159 ASP cc_start: 0.7518 (m-30) cc_final: 0.7075 (m-30) REVERT: F 231 ARG cc_start: 0.7605 (mtm180) cc_final: 0.7363 (mtm180) REVERT: G 119 LYS cc_start: 0.6335 (tptp) cc_final: 0.5582 (tptm) REVERT: G 231 ARG cc_start: 0.7533 (ttm110) cc_final: 0.7007 (ttp80) REVERT: H 163 ASP cc_start: 0.8050 (m-30) cc_final: 0.7530 (m-30) REVERT: H 203 ASP cc_start: 0.8023 (t0) cc_final: 0.7765 (t0) REVERT: H 229 MET cc_start: 0.8285 (mmm) cc_final: 0.7868 (mpp) REVERT: h 577 GLN cc_start: 0.6823 (tt0) cc_final: 0.6292 (tm-30) REVERT: I 206 ASN cc_start: 0.8123 (m-40) cc_final: 0.7905 (m-40) REVERT: I 231 ARG cc_start: 0.7220 (ttm110) cc_final: 0.6780 (mtm-85) REVERT: I 238 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7805 (mt-10) REVERT: i 579 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7283 (mtt90) REVERT: J 20 TRP cc_start: 0.7166 (t60) cc_final: 0.6932 (t60) REVERT: J 81 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6304 (mt0) REVERT: J 160 ILE cc_start: 0.8714 (mt) cc_final: 0.8303 (mm) REVERT: j 574 ASP cc_start: 0.8020 (t0) cc_final: 0.7818 (t0) outliers start: 36 outliers final: 25 residues processed: 364 average time/residue: 0.1968 time to fit residues: 106.3940 Evaluate side-chains 342 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 316 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain b residue 578 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 117 VAL 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 153 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 81 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 29 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 185 optimal weight: 0.0770 chunk 240 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN D 269 GLN E 38 GLN J 38 GLN ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102196 restraints weight = 30064.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104188 restraints weight = 32353.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104568 restraints weight = 26089.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.104971 restraints weight = 22162.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105205 restraints weight = 20270.643| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23496 Z= 0.201 Angle : 0.595 8.106 31799 Z= 0.308 Chirality : 0.043 0.222 3531 Planarity : 0.004 0.037 3858 Dihedral : 16.520 179.769 3794 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.15 % Allowed : 14.06 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.16), residues: 2670 helix: 1.73 (0.13), residues: 1600 sheet: 1.68 (0.27), residues: 280 loop : -0.13 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 579 TYR 0.014 0.001 TYR a 575 PHE 0.013 0.002 PHE C 125 TRP 0.013 0.002 TRP F 20 HIS 0.006 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00486 (23487) covalent geometry : angle 0.59537 (31799) hydrogen bonds : bond 0.04722 ( 1147) hydrogen bonds : angle 4.45229 ( 3285) Misc. bond : bond 0.00385 ( 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 367 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 316 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6874 (tt) REVERT: A 107 LYS cc_start: 0.7907 (tttm) cc_final: 0.7484 (ttpt) REVERT: A 113 LEU cc_start: 0.8652 (mt) cc_final: 0.8193 (mt) REVERT: B 230 LEU cc_start: 0.8660 (mt) cc_final: 0.8443 (tp) REVERT: C 182 ARG cc_start: 0.7406 (ttm-80) cc_final: 0.6782 (ttp-110) REVERT: D 113 LEU cc_start: 0.8506 (mt) cc_final: 0.8164 (mt) REVERT: D 203 ASP cc_start: 0.7930 (t0) cc_final: 0.7612 (t0) REVERT: D 230 LEU cc_start: 0.8666 (mt) cc_final: 0.8291 (tp) REVERT: D 246 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6961 (mt-10) REVERT: D 250 GLU cc_start: 0.8011 (tp30) cc_final: 0.7719 (tt0) REVERT: E 47 ASP cc_start: 0.7422 (m-30) cc_final: 0.7153 (m-30) REVERT: E 159 ASP cc_start: 0.8029 (m-30) cc_final: 0.7299 (m-30) REVERT: E 181 LYS cc_start: 0.8264 (mttt) cc_final: 0.7693 (mtmt) REVERT: E 229 MET cc_start: 0.7575 (mmt) cc_final: 0.7290 (mtt) REVERT: G 64 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8368 (p) REVERT: G 231 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7084 (ttp80) REVERT: H 99 LYS cc_start: 0.7487 (mttt) cc_final: 0.7197 (mttp) REVERT: H 131 GLU cc_start: 0.7273 (tt0) cc_final: 0.7040 (tt0) REVERT: H 163 ASP cc_start: 0.8205 (m-30) cc_final: 0.7673 (m-30) REVERT: H 203 ASP cc_start: 0.8156 (t0) cc_final: 0.7855 (t0) REVERT: H 229 MET cc_start: 0.8496 (mmm) cc_final: 0.8063 (mpp) REVERT: I 206 ASN cc_start: 0.8307 (m-40) cc_final: 0.7807 (m-40) REVERT: I 231 ARG cc_start: 0.7272 (ttm110) cc_final: 0.6877 (mtm-85) REVERT: I 261 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7639 (mmtm) REVERT: J 20 TRP cc_start: 0.7418 (t60) cc_final: 0.7184 (t60) REVERT: J 81 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6819 (mt0) REVERT: J 85 ARG cc_start: 0.6515 (mmt90) cc_final: 0.5978 (mtp180) REVERT: J 160 ILE cc_start: 0.8849 (mt) cc_final: 0.8482 (mm) REVERT: j 574 ASP cc_start: 0.8195 (t0) cc_final: 0.7942 (t0) outliers start: 51 outliers final: 36 residues processed: 355 average time/residue: 0.1848 time to fit residues: 96.9478 Evaluate side-chains 340 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 301 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 34 VAL 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 235 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain b residue 578 LEU Chi-restraints excluded: chain C residue 64 THR 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 D residue 117 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 253 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 195 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 258 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN F 206 ASN H 223 ASN J 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106226 restraints weight = 29897.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107227 restraints weight = 31979.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.108225 restraints weight = 27269.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108310 restraints weight = 22616.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108379 restraints weight = 21560.875| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23496 Z= 0.141 Angle : 0.537 8.688 31799 Z= 0.281 Chirality : 0.041 0.211 3531 Planarity : 0.004 0.036 3858 Dihedral : 16.387 179.800 3794 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.15 % Allowed : 14.35 % Favored : 83.50 % 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 aren not related in a simple way. whole: 1.84 (0.16), residues: 2670 helix: 1.84 (0.13), residues: 1600 sheet: 1.60 (0.27), residues: 280 loop : -0.14 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 579 TYR 0.010 0.001 TYR a 575 PHE 0.010 0.001 PHE C 125 TRP 0.014 0.001 TRP C 45 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00331 (23487) covalent geometry : angle 0.53728 (31799) hydrogen bonds : bond 0.03868 ( 1147) hydrogen bonds : angle 4.35435 ( 3285) Misc. bond : bond 0.00291 ( 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 368 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7846 (tttm) cc_final: 0.7440 (ttpt) REVERT: A 113 LEU cc_start: 0.8575 (mt) cc_final: 0.8131 (mt) REVERT: A 205 LYS cc_start: 0.8455 (tmmt) cc_final: 0.8239 (tptp) REVERT: C 182 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.6805 (ttp-110) REVERT: C 230 LEU cc_start: 0.8402 (mt) cc_final: 0.8107 (tp) REVERT: D 113 LEU cc_start: 0.8418 (mt) cc_final: 0.8060 (mt) REVERT: D 203 ASP cc_start: 0.7883 (t0) cc_final: 0.7618 (t0) REVERT: D 230 LEU cc_start: 0.8597 (mt) cc_final: 0.8281 (tp) REVERT: D 250 GLU cc_start: 0.7941 (tp30) cc_final: 0.7626 (tt0) REVERT: E 47 ASP cc_start: 0.7371 (m-30) cc_final: 0.7103 (m-30) REVERT: E 159 ASP cc_start: 0.7990 (m-30) cc_final: 0.7255 (m-30) REVERT: E 181 LYS cc_start: 0.8231 (mttt) cc_final: 0.7658 (mtmt) REVERT: E 229 MET cc_start: 0.7489 (mmt) cc_final: 0.7224 (mtt) REVERT: F 159 ASP cc_start: 0.7499 (m-30) cc_final: 0.7113 (m-30) REVERT: G 119 LYS cc_start: 0.6475 (tptp) cc_final: 0.5676 (tttp) REVERT: G 231 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7077 (ttp80) REVERT: H 99 LYS cc_start: 0.7486 (mttt) cc_final: 0.7212 (mttp) REVERT: H 131 GLU cc_start: 0.7208 (tt0) cc_final: 0.6997 (tt0) REVERT: H 163 ASP cc_start: 0.8122 (m-30) cc_final: 0.7593 (m-30) REVERT: H 203 ASP cc_start: 0.8055 (t0) cc_final: 0.7826 (t0) REVERT: H 229 MET cc_start: 0.8468 (mmm) cc_final: 0.8085 (mpp) REVERT: h 577 GLN cc_start: 0.6779 (tm-30) cc_final: 0.5718 (tm-30) REVERT: I 206 ASN cc_start: 0.8311 (m-40) cc_final: 0.7860 (m-40) REVERT: I 231 ARG cc_start: 0.7297 (ttm110) cc_final: 0.6871 (mtm-85) REVERT: I 261 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7420 (mmtm) REVERT: J 20 TRP cc_start: 0.7330 (t60) cc_final: 0.7126 (t60) REVERT: J 85 ARG cc_start: 0.6319 (mmt90) cc_final: 0.5961 (mtp180) REVERT: J 160 ILE cc_start: 0.8787 (mt) cc_final: 0.8420 (mm) REVERT: j 574 ASP cc_start: 0.8198 (t0) cc_final: 0.7948 (t0) outliers start: 51 outliers final: 39 residues processed: 353 average time/residue: 0.1935 time to fit residues: 100.6896 Evaluate side-chains 340 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 301 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 235 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 64 THR 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 D residue 117 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 261 LYS Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain h residue 572 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 223 ASN Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 253 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 103 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 247 optimal weight: 0.7980 chunk 106 optimal weight: 0.0970 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN H 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.107992 restraints weight = 30128.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108275 restraints weight = 31722.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108899 restraints weight = 30830.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.109385 restraints weight = 25411.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109511 restraints weight = 23276.118| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23496 Z= 0.116 Angle : 0.513 8.177 31799 Z= 0.269 Chirality : 0.040 0.190 3531 Planarity : 0.003 0.036 3858 Dihedral : 16.211 179.635 3794 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.82 % Allowed : 14.86 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.16), residues: 2670 helix: 1.92 (0.13), residues: 1610 sheet: 1.56 (0.27), residues: 280 loop : 0.06 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 579 TYR 0.009 0.001 TYR j 575 PHE 0.007 0.001 PHE C 125 TRP 0.019 0.001 TRP B 20 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00262 (23487) covalent geometry : angle 0.51267 (31799) hydrogen bonds : bond 0.03481 ( 1147) hydrogen bonds : angle 4.32113 ( 3285) Misc. bond : bond 0.00257 ( 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 363 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 0.932 Fit side-chains REVERT: A 21 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6864 (tt) REVERT: A 107 LYS cc_start: 0.7892 (tttm) cc_final: 0.7433 (ttpt) REVERT: A 113 LEU cc_start: 0.8539 (mt) cc_final: 0.8087 (mt) REVERT: A 116 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7442 (tpt170) REVERT: A 206 ASN cc_start: 0.8569 (m-40) cc_final: 0.8297 (m110) REVERT: C 180 ILE cc_start: 0.8510 (tt) cc_final: 0.8174 (tt) REVERT: C 182 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.6698 (ttp-110) REVERT: C 230 LEU cc_start: 0.8358 (mt) cc_final: 0.8055 (tp) REVERT: D 113 LEU cc_start: 0.8318 (mt) cc_final: 0.7937 (mt) REVERT: D 128 ARG cc_start: 0.7362 (tpt170) cc_final: 0.7068 (tpm170) REVERT: D 203 ASP cc_start: 0.7913 (t0) cc_final: 0.7682 (t0) REVERT: D 230 LEU cc_start: 0.8562 (mt) cc_final: 0.8267 (tp) REVERT: D 250 GLU cc_start: 0.7811 (tp30) cc_final: 0.7508 (tt0) REVERT: E 47 ASP cc_start: 0.7360 (m-30) cc_final: 0.7094 (m-30) REVERT: E 159 ASP cc_start: 0.7974 (m-30) cc_final: 0.7228 (m-30) REVERT: E 181 LYS cc_start: 0.8121 (mttt) cc_final: 0.7674 (mtmt) REVERT: E 229 MET cc_start: 0.7503 (mmt) cc_final: 0.7248 (mtt) REVERT: F 159 ASP cc_start: 0.7351 (m-30) cc_final: 0.6953 (m-30) REVERT: F 231 ARG cc_start: 0.7681 (mtm180) cc_final: 0.7455 (mtm180) REVERT: G 78 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7410 (mmpt) REVERT: G 119 LYS cc_start: 0.6433 (tptp) cc_final: 0.5542 (tttp) REVERT: G 231 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7052 (ttp80) REVERT: H 99 LYS cc_start: 0.7449 (mttt) cc_final: 0.7187 (mttp) REVERT: H 131 GLU cc_start: 0.7193 (tt0) cc_final: 0.6990 (tt0) REVERT: H 163 ASP cc_start: 0.8068 (m-30) cc_final: 0.7557 (m-30) REVERT: H 212 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6934 (tm-30) REVERT: H 223 ASN cc_start: 0.8457 (t0) cc_final: 0.8248 (t0) REVERT: H 229 MET cc_start: 0.8460 (mmm) cc_final: 0.8077 (mpp) REVERT: h 577 GLN cc_start: 0.7189 (tm-30) cc_final: 0.6054 (tm-30) REVERT: h 581 GLU cc_start: 0.4809 (mt-10) cc_final: 0.3812 (mt-10) REVERT: I 113 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7979 (mm) REVERT: I 206 ASN cc_start: 0.8403 (m-40) cc_final: 0.8014 (m-40) REVERT: I 231 ARG cc_start: 0.7284 (ttm110) cc_final: 0.6858 (mtm-85) REVERT: I 261 LYS cc_start: 0.7641 (mmtt) cc_final: 0.7365 (mmtm) REVERT: i 579 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7252 (mtt90) REVERT: J 20 TRP cc_start: 0.7368 (t60) cc_final: 0.7155 (t60) REVERT: J 64 THR cc_start: 0.8799 (p) cc_final: 0.8481 (p) REVERT: J 85 ARG cc_start: 0.6302 (mmt90) cc_final: 0.5794 (mtp180) REVERT: J 140 MET cc_start: 0.9206 (ttp) cc_final: 0.8916 (ttm) REVERT: J 160 ILE cc_start: 0.8716 (mt) cc_final: 0.8337 (mm) REVERT: j 574 ASP cc_start: 0.8161 (t0) cc_final: 0.7958 (t0) outliers start: 43 outliers final: 35 residues processed: 353 average time/residue: 0.1699 time to fit residues: 89.6710 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 : 0.811 ------------------------------------------------------------------------------- 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 235 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 64 THR 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 D residue 117 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 223 ASN Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 184 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 43 optimal weight: 0.9990 chunk 196 optimal weight: 0.0070 chunk 230 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN F 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108339 restraints weight = 29746.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109883 restraints weight = 32533.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.110583 restraints weight = 26863.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110845 restraints weight = 22138.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.110953 restraints weight = 21514.278| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23496 Z= 0.101 Angle : 0.498 8.655 31799 Z= 0.262 Chirality : 0.039 0.186 3531 Planarity : 0.003 0.035 3858 Dihedral : 15.977 178.798 3794 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.31 % Allowed : 15.45 % Favored : 83.24 % 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 aren not related in a simple way. whole: 2.20 (0.16), residues: 2670 helix: 2.10 (0.13), residues: 1600 sheet: 1.63 (0.26), residues: 280 loop : 0.13 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 579 TYR 0.008 0.001 TYR j 575 PHE 0.011 0.001 PHE A 204 TRP 0.018 0.001 TRP A 211 HIS 0.004 0.000 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00222 (23487) covalent geometry : angle 0.49843 (31799) hydrogen bonds : bond 0.03075 ( 1147) hydrogen bonds : angle 4.24861 ( 3285) Misc. bond : bond 0.00216 ( 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: 31 poor density : 321 time to evaluate : 0.574 Fit side-chains REVERT: A 21 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6823 (tt) REVERT: A 107 LYS cc_start: 0.7799 (tttm) cc_final: 0.7409 (ttpt) REVERT: A 113 LEU cc_start: 0.8589 (mt) cc_final: 0.8135 (mt) REVERT: A 116 ARG cc_start: 0.7716 (mmm160) cc_final: 0.7435 (tpt170) REVERT: A 206 ASN cc_start: 0.8615 (m-40) cc_final: 0.8373 (m110) REVERT: C 180 ILE cc_start: 0.8502 (tt) cc_final: 0.8160 (tt) REVERT: C 182 ARG cc_start: 0.7368 (ttm-80) cc_final: 0.6707 (ttp-110) REVERT: C 230 LEU cc_start: 0.8332 (mt) cc_final: 0.8033 (tp) REVERT: D 113 LEU cc_start: 0.8157 (mt) cc_final: 0.7773 (mt) REVERT: D 128 ARG cc_start: 0.7450 (tpt170) cc_final: 0.7132 (tpm170) REVERT: D 250 GLU cc_start: 0.7775 (tp30) cc_final: 0.7482 (mt-10) REVERT: d 576 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7522 (mm-30) REVERT: E 159 ASP cc_start: 0.7835 (m-30) cc_final: 0.7160 (m-30) REVERT: E 181 LYS cc_start: 0.8022 (mttt) cc_final: 0.7462 (mtmt) REVERT: E 229 MET cc_start: 0.7434 (mmt) cc_final: 0.7191 (mtt) REVERT: F 159 ASP cc_start: 0.7403 (m-30) cc_final: 0.7126 (m-30) REVERT: F 231 ARG cc_start: 0.7715 (mtm180) cc_final: 0.7457 (mtm180) REVERT: G 231 ARG cc_start: 0.7528 (ttm110) cc_final: 0.7001 (ttp80) REVERT: H 163 ASP cc_start: 0.8005 (m-30) cc_final: 0.7469 (m-30) REVERT: H 212 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6822 (tm-30) REVERT: H 229 MET cc_start: 0.8361 (mmm) cc_final: 0.7961 (mpp) REVERT: h 577 GLN cc_start: 0.7229 (tm-30) cc_final: 0.6092 (tm-30) REVERT: h 581 GLU cc_start: 0.4940 (mt-10) cc_final: 0.3955 (mt-10) REVERT: I 28 LEU cc_start: 0.7758 (mt) cc_final: 0.7431 (mt) REVERT: I 113 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7939 (mm) REVERT: I 140 MET cc_start: 0.9112 (ttp) cc_final: 0.8879 (ttp) REVERT: I 206 ASN cc_start: 0.8375 (m-40) cc_final: 0.8054 (m-40) REVERT: I 225 LYS cc_start: 0.6891 (tptt) cc_final: 0.6581 (ptpp) REVERT: I 231 ARG cc_start: 0.7236 (ttm110) cc_final: 0.6797 (mtm-85) REVERT: I 261 LYS cc_start: 0.7427 (mmtt) cc_final: 0.7199 (mmtm) REVERT: i 579 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7304 (mtt90) REVERT: J 20 TRP cc_start: 0.7290 (t60) cc_final: 0.7080 (t60) REVERT: J 85 ARG cc_start: 0.6289 (mmt90) cc_final: 0.5858 (mtp180) REVERT: J 140 MET cc_start: 0.9168 (ttp) cc_final: 0.8885 (ttm) REVERT: J 160 ILE cc_start: 0.8647 (mt) cc_final: 0.8221 (mm) REVERT: J 221 SER cc_start: 0.6643 (p) cc_final: 0.6259 (m) outliers start: 31 outliers final: 25 residues processed: 345 average time/residue: 0.1663 time to fit residues: 85.6136 Evaluate side-chains 338 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 311 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 255 SER Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 184 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.594 > 50: distance: 100 - 101: 3.908 distance: 101 - 104: 3.632 distance: 102 - 107: 4.622 distance: 104 - 106: 3.323 distance: 107 - 108: 6.152 distance: 108 - 109: 3.757 distance: 108 - 111: 3.289 distance: 109 - 110: 9.780 distance: 109 - 116: 8.521 distance: 111 - 112: 4.878 distance: 113 - 114: 6.233 distance: 113 - 115: 3.139 distance: 117 - 118: 8.988 distance: 117 - 120: 3.906 distance: 118 - 119: 4.212 distance: 118 - 124: 12.212 distance: 121 - 122: 4.209 distance: 122 - 123: 4.037 distance: 124 - 213: 5.267 distance: 125 - 126: 8.772 distance: 125 - 128: 4.459 distance: 126 - 127: 9.816 distance: 126 - 132: 8.399 distance: 127 - 222: 16.035 distance: 128 - 129: 6.134 distance: 129 - 130: 4.500 distance: 129 - 131: 6.315 distance: 133 - 134: 10.940 distance: 133 - 136: 12.799 distance: 134 - 135: 11.825 distance: 134 - 140: 5.418 distance: 136 - 137: 12.130 distance: 136 - 138: 9.728 distance: 137 - 139: 6.764 distance: 140 - 141: 6.177 distance: 140 - 225: 7.845 distance: 141 - 144: 5.093 distance: 142 - 143: 10.773 distance: 142 - 148: 18.911 distance: 143 - 237: 13.633 distance: 144 - 145: 8.170 distance: 144 - 146: 6.931 distance: 145 - 147: 14.080 distance: 148 - 149: 11.602 distance: 149 - 150: 6.773 distance: 149 - 152: 6.927 distance: 150 - 151: 13.921 distance: 150 - 156: 23.018 distance: 152 - 153: 7.439 distance: 153 - 154: 6.707 distance: 153 - 155: 4.665 distance: 156 - 157: 14.096 distance: 157 - 158: 16.708 distance: 157 - 160: 13.002 distance: 158 - 159: 7.505 distance: 158 - 165: 11.855 distance: 159 - 178: 15.504 distance: 160 - 161: 11.580 distance: 161 - 162: 6.137 distance: 162 - 163: 4.234 distance: 162 - 164: 3.836 distance: 165 - 166: 5.269 distance: 166 - 167: 24.618 distance: 166 - 169: 32.605 distance: 167 - 168: 24.438 distance: 167 - 170: 8.848 distance: 168 - 189: 22.159 distance: 170 - 171: 8.652 distance: 171 - 172: 9.736 distance: 171 - 174: 16.855 distance: 172 - 178: 4.015 distance: 174 - 175: 9.259 distance: 175 - 176: 8.243 distance: 175 - 177: 10.921