Starting phenix.real_space_refine on Thu Jun 19 20:50:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7svv_25454/06_2025/7svv_25454.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svv_25454/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7svv_25454/06_2025/7svv_25454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svv_25454/06_2025/7svv_25454.map" model { file = "/net/cci-nas-00/data/ceres_data/7svv_25454/06_2025/7svv_25454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svv_25454/06_2025/7svv_25454.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.00, per 1000 atoms: 0.56 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: 6.54 Conformation dependent library (CDL) restraints added in 2.6 seconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 20 sheets defined 61.7% alpha, 7.4% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 7.10 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: 6.79 Time building geometry restraints manager: 7.26 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: 0.700 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: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 54.080 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.002 TRP B 45 HIS 0.001 0.000 HIS H 77 PHE 0.007 0.001 PHE E 196 TYR 0.016 0.002 TYR J 112 ARG 0.003 0.000 ARG F 249 Details of bonding type rmsd hydrogen bonds : bond 0.24473 ( 1147) hydrogen bonds : angle 7.91435 ( 3285) covalent geometry : bond 0.02033 (23487) covalent geometry : angle 1.87664 (31799) 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 : 2.749 Fit side-chains 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: 0.7511 (ttm110) REVERT: B 40 LYS cc_start: 0.8168 (tptp) cc_final: 0.7947 (ttmt) REVERT: B 47 ASP cc_start: 0.7479 (t70) cc_final: 0.7186 (t0) REVERT: B 54 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7566 (tttp) REVERT: B 188 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7877 (mm-30) REVERT: B 230 LEU cc_start: 0.8705 (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: 0.5655 (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: 0.7610 (t0) REVERT: F 54 LYS cc_start: 0.8306 (mmtm) cc_final: 0.7985 (tttm) REVERT: F 140 MET cc_start: 0.9285 (ttm) cc_final: 0.9052 (ttp) REVERT: F 159 ASP cc_start: 0.6987 (m-30) cc_final: 0.6530 (m-30) REVERT: F 163 ASP cc_start: 0.8125 (m-30) cc_final: 0.7854 (m-30) REVERT: F 229 MET cc_start: 0.8570 (mmm) cc_final: 0.8233 (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: 0.6094 (tppt) REVERT: G 139 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8103 (mt-10) REVERT: G 162 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6054 (mm-30) REVERT: G 231 ARG cc_start: 0.7312 (ttm110) cc_final: 0.7109 (ttp80) REVERT: H 107 LYS cc_start: 0.8113 (tttm) cc_final: 0.7724 (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: 0.7463 (mt-10) REVERT: h 582 TYR cc_start: 0.6758 (t80) cc_final: 0.6329 (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: 0.7806 (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: 0.7483 (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: 0.5202 time to fit residues: 517.5207 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 : 4.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.148182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115445 restraints weight = 30123.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116561 restraints weight = 32830.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117690 restraints weight = 26890.760| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3695 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= 0.130 Angle : 0.570 7.047 31799 Z= 0.304 Chirality : 0.041 0.228 3531 Planarity : 0.005 0.034 3858 Dihedral : 17.223 179.089 3794 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.65 % Allowed : 8.48 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 2670 helix: 1.44 (0.13), residues: 1600 sheet: 2.65 (0.31), residues: 230 loop : 0.10 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 45 HIS 0.004 0.001 HIS I 97 PHE 0.008 0.001 PHE A 106 TYR 0.013 0.001 TYR j 575 ARG 0.007 0.000 ARG j 579 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 1147) hydrogen bonds : angle 4.58986 ( 3285) covalent geometry : bond 0.00280 (23487) covalent geometry : angle 0.56979 (31799) Misc. bond : bond 0.00287 ( 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: 39 poor density : 406 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7434 (tttm) cc_final: 0.6888 (ttpt) REVERT: A 113 LEU cc_start: 0.8574 (mt) cc_final: 0.7911 (mt) REVERT: A 127 ASP cc_start: 0.6972 (m-30) cc_final: 0.6608 (m-30) REVERT: A 203 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7827 (t0) REVERT: A 205 LYS cc_start: 0.8229 (tmmt) cc_final: 0.7978 (tptp) REVERT: B 211 TRP cc_start: 0.8523 (t-100) cc_final: 0.8244 (t-100) REVERT: B 230 LEU cc_start: 0.8800 (mt) cc_final: 0.8488 (tp) REVERT: B 268 LEU cc_start: 0.8877 (tp) cc_final: 0.8671 (tt) REVERT: b 571 GLU cc_start: 0.6824 (pm20) cc_final: 0.6611 (pm20) REVERT: C 153 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7906 (t) REVERT: C 182 ARG cc_start: 0.7146 (ttm-80) cc_final: 0.6582 (ttp-110) REVERT: C 230 LEU cc_start: 0.8163 (mt) cc_final: 0.7946 (tp) REVERT: D 113 LEU cc_start: 0.8370 (mt) cc_final: 0.8148 (mt) REVERT: D 203 ASP cc_start: 0.7620 (t0) cc_final: 0.7268 (t0) REVERT: D 229 MET cc_start: 0.8171 (mmm) cc_final: 0.7890 (mmt) REVERT: D 230 LEU cc_start: 0.8661 (mt) cc_final: 0.8312 (tp) REVERT: D 250 GLU cc_start: 0.7893 (tp30) cc_final: 0.7513 (tt0) REVERT: E 181 LYS cc_start: 0.8197 (mttt) cc_final: 0.7847 (mtmt) REVERT: F 140 MET cc_start: 0.9059 (ttm) cc_final: 0.8820 (ttt) REVERT: F 159 ASP cc_start: 0.7530 (m-30) cc_final: 0.7014 (m-30) REVERT: G 27 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7644 (ttp80) REVERT: G 33 ILE cc_start: 0.9017 (mt) cc_final: 0.8815 (mm) REVERT: G 54 LYS cc_start: 0.7891 (mmtm) cc_final: 0.7670 (mtpp) REVERT: G 76 ARG cc_start: 0.7393 (mtp180) cc_final: 0.6846 (mtp180) REVERT: G 113 LEU cc_start: 0.7692 (mt) cc_final: 0.7379 (mt) REVERT: G 159 ASP cc_start: 0.7721 (m-30) cc_final: 0.7473 (m-30) REVERT: G 231 ARG cc_start: 0.7164 (ttm110) cc_final: 0.6826 (ttp80) REVERT: H 159 ASP cc_start: 0.7393 (m-30) cc_final: 0.6887 (m-30) REVERT: H 163 ASP cc_start: 0.7996 (m-30) cc_final: 0.7736 (m-30) REVERT: H 203 ASP cc_start: 0.7902 (t0) cc_final: 0.7632 (t0) REVERT: I 206 ASN cc_start: 0.7807 (m-40) cc_final: 0.7599 (m-40) REVERT: I 238 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7778 (mt-10) REVERT: J 78 LYS cc_start: 0.7949 (mttt) cc_final: 0.7305 (mtpt) REVERT: J 261 LYS cc_start: 0.6274 (mmtt) cc_final: 0.5919 (ttpp) REVERT: J 269 GLN cc_start: 0.7589 (mt0) cc_final: 0.7229 (mt0) outliers start: 39 outliers final: 19 residues processed: 423 average time/residue: 0.4261 time to fit residues: 261.1800 Evaluate side-chains 339 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 318 time to evaluate : 2.674 ------------------------------------------------------------------------------- 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 C residue 153 THR 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 248 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 204 optimal weight: 0.1980 chunk 220 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 202 optimal weight: 0.2980 chunk 192 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN F 206 ASN G 269 GLN I 269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112024 restraints weight = 30101.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113083 restraints weight = 31589.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114124 restraints weight = 26802.827| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4402 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= 0.104 Angle : 0.496 6.273 31799 Z= 0.263 Chirality : 0.040 0.218 3531 Planarity : 0.004 0.035 3858 Dihedral : 16.307 176.817 3794 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.14 % Allowed : 10.72 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.16), residues: 2670 helix: 2.03 (0.13), residues: 1600 sheet: 2.22 (0.28), residues: 280 loop : 0.20 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 45 HIS 0.003 0.001 HIS J 77 PHE 0.007 0.001 PHE H 190 TYR 0.010 0.001 TYR a 575 ARG 0.007 0.000 ARG j 579 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 1147) hydrogen bonds : angle 4.27778 ( 3285) covalent geometry : bond 0.00218 (23487) covalent geometry : angle 0.49618 (31799) Misc. bond : bond 0.00250 ( 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 395 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 368 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7455 (tttm) cc_final: 0.7096 (ttpt) REVERT: A 203 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7774 (t0) REVERT: A 205 LYS cc_start: 0.8380 (tmmt) cc_final: 0.8082 (tptp) REVERT: B 211 TRP cc_start: 0.8553 (t-100) cc_final: 0.8304 (t-100) REVERT: B 230 LEU cc_start: 0.8733 (mt) cc_final: 0.8473 (tp) REVERT: C 182 ARG cc_start: 0.7222 (ttm-80) cc_final: 0.6682 (ttp-110) REVERT: C 230 LEU cc_start: 0.8200 (mt) cc_final: 0.7988 (tp) REVERT: D 113 LEU cc_start: 0.8217 (mt) cc_final: 0.7913 (mt) REVERT: D 203 ASP cc_start: 0.7942 (t0) cc_final: 0.7564 (t0) REVERT: D 229 MET cc_start: 0.8269 (mmm) cc_final: 0.7989 (mmt) REVERT: D 230 LEU cc_start: 0.8609 (mt) cc_final: 0.8260 (tp) REVERT: D 250 GLU cc_start: 0.7844 (tp30) cc_final: 0.7477 (tt0) REVERT: E 181 LYS cc_start: 0.8117 (mttt) cc_final: 0.7773 (mtmt) REVERT: F 159 ASP cc_start: 0.7491 (m-30) cc_final: 0.6980 (m-30) REVERT: F 191 ARG cc_start: 0.8215 (ttt90) cc_final: 0.7927 (ttt90) REVERT: F 255 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8326 (m) REVERT: G 27 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7518 (ttt-90) REVERT: G 214 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7147 (mtp) REVERT: G 231 ARG cc_start: 0.7435 (ttm110) cc_final: 0.7025 (ttp80) REVERT: G 255 SER cc_start: 0.7653 (OUTLIER) cc_final: 0.7425 (m) REVERT: G 269 GLN cc_start: 0.8003 (tp40) cc_final: 0.7751 (tp-100) REVERT: H 131 GLU cc_start: 0.6415 (tp30) cc_final: 0.5809 (tp30) REVERT: H 163 ASP cc_start: 0.8059 (m-30) cc_final: 0.7702 (m-30) REVERT: H 203 ASP cc_start: 0.7981 (t0) cc_final: 0.7724 (t0) REVERT: I 206 ASN cc_start: 0.7835 (m-40) cc_final: 0.7536 (m-40) REVERT: I 223 ASN cc_start: 0.6551 (m110) cc_final: 0.5887 (t0) REVERT: I 238 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7750 (mt-10) REVERT: J 223 ASN cc_start: 0.6893 (m-40) cc_final: 0.6501 (t0) REVERT: J 269 GLN cc_start: 0.7692 (mt0) cc_final: 0.7429 (mt0) outliers start: 27 outliers final: 12 residues processed: 383 average time/residue: 0.4187 time to fit residues: 232.1332 Evaluate side-chains 326 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 310 time to evaluate : 2.707 ------------------------------------------------------------------------------- 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 64 THR Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 103 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 170 optimal weight: 0.8980 chunk 122 optimal weight: 0.2980 chunk 103 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.106966 restraints weight = 30342.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.108469 restraints weight = 32240.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109265 restraints weight = 25517.752| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23496 Z= 0.134 Angle : 0.523 5.907 31799 Z= 0.276 Chirality : 0.041 0.212 3531 Planarity : 0.004 0.041 3858 Dihedral : 16.405 177.752 3794 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.73 % Allowed : 11.95 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.16), residues: 2670 helix: 1.97 (0.13), residues: 1610 sheet: 2.08 (0.28), residues: 280 loop : 0.08 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 20 HIS 0.004 0.001 HIS G 77 PHE 0.008 0.001 PHE D 125 TYR 0.008 0.001 TYR a 575 ARG 0.007 0.000 ARG j 579 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 1147) hydrogen bonds : angle 4.29669 ( 3285) covalent geometry : bond 0.00306 (23487) covalent geometry : angle 0.52337 (31799) Misc. bond : bond 0.00304 ( 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 382 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7819 (tttm) cc_final: 0.7140 (ttpt) REVERT: A 113 LEU cc_start: 0.8630 (mt) cc_final: 0.8143 (mt) REVERT: A 205 LYS cc_start: 0.8402 (tmmt) cc_final: 0.8173 (tptp) REVERT: B 211 TRP cc_start: 0.8630 (OUTLIER) cc_final: 0.8331 (t-100) REVERT: B 230 LEU cc_start: 0.8687 (mt) cc_final: 0.8411 (tp) REVERT: C 182 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6694 (ttp-110) REVERT: C 230 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7827 (tp) REVERT: D 113 LEU cc_start: 0.8261 (mt) cc_final: 0.7935 (mt) REVERT: D 203 ASP cc_start: 0.7953 (t0) cc_final: 0.7614 (t0) REVERT: D 229 MET cc_start: 0.8339 (mmm) cc_final: 0.7993 (mmt) REVERT: D 230 LEU cc_start: 0.8700 (mt) cc_final: 0.8249 (tp) REVERT: D 250 GLU cc_start: 0.7894 (tp30) cc_final: 0.7521 (tt0) REVERT: D 262 LYS cc_start: 0.8019 (pttt) cc_final: 0.7755 (ptmt) REVERT: E 159 ASP cc_start: 0.7906 (m-30) cc_final: 0.6976 (m-30) REVERT: E 181 LYS cc_start: 0.8198 (mttt) cc_final: 0.7789 (mtmt) REVERT: F 159 ASP cc_start: 0.7648 (m-30) cc_final: 0.7185 (m-30) REVERT: F 255 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8233 (m) REVERT: F 264 ASP cc_start: 0.7490 (p0) cc_final: 0.7190 (t0) REVERT: G 62 SER cc_start: 0.8187 (t) cc_final: 0.7888 (m) REVERT: G 231 ARG cc_start: 0.7506 (ttm110) cc_final: 0.7009 (ttp80) REVERT: H 131 GLU cc_start: 0.6666 (tp30) cc_final: 0.6237 (tp30) REVERT: H 163 ASP cc_start: 0.8104 (m-30) cc_final: 0.7662 (m-30) REVERT: I 223 ASN cc_start: 0.7061 (m110) cc_final: 0.6527 (m-40) REVERT: I 238 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7775 (mt-10) REVERT: J 20 TRP cc_start: 0.7235 (t60) cc_final: 0.6922 (t60) REVERT: J 160 ILE cc_start: 0.8675 (mt) cc_final: 0.8243 (mm) outliers start: 41 outliers final: 25 residues processed: 365 average time/residue: 0.4114 time to fit residues: 222.5351 Evaluate side-chains 333 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 305 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 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 230 LEU 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 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 260 LEU Chi-restraints excluded: chain h residue 572 VAL Chi-restraints excluded: chain I residue 25 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 65 optimal weight: 0.9990 chunk 242 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 192 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN G 98 GLN H 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108916 restraints weight = 30123.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110444 restraints weight = 31274.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111004 restraints weight = 25663.705| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23496 Z= 0.104 Angle : 0.480 6.830 31799 Z= 0.255 Chirality : 0.040 0.198 3531 Planarity : 0.003 0.036 3858 Dihedral : 16.274 177.928 3794 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.44 % Allowed : 13.21 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.16), residues: 2670 helix: 2.02 (0.13), residues: 1620 sheet: 1.97 (0.27), residues: 280 loop : 0.15 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 45 HIS 0.002 0.001 HIS G 77 PHE 0.005 0.001 PHE C 125 TYR 0.006 0.001 TYR j 575 ARG 0.007 0.000 ARG d 579 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 1147) hydrogen bonds : angle 4.21085 ( 3285) covalent geometry : bond 0.00229 (23487) covalent geometry : angle 0.47967 (31799) Misc. bond : bond 0.00231 ( 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 376 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 342 time to evaluate : 2.496 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7738 (tttm) cc_final: 0.7152 (ttpt) REVERT: A 113 LEU cc_start: 0.8427 (mt) cc_final: 0.8017 (mt) REVERT: A 127 ASP cc_start: 0.7112 (m-30) cc_final: 0.6689 (m-30) REVERT: A 205 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8198 (tptp) REVERT: B 211 TRP cc_start: 0.8632 (OUTLIER) cc_final: 0.8385 (t-100) REVERT: B 230 LEU cc_start: 0.8757 (mt) cc_final: 0.8408 (tp) REVERT: C 182 ARG cc_start: 0.7287 (ttm-80) cc_final: 0.6707 (ttp-110) REVERT: C 230 LEU cc_start: 0.8274 (mt) cc_final: 0.8016 (tp) REVERT: D 113 LEU cc_start: 0.8152 (mt) cc_final: 0.7826 (mt) REVERT: D 128 ARG cc_start: 0.7191 (tpt170) cc_final: 0.6765 (tpt170) REVERT: D 203 ASP cc_start: 0.7979 (t0) cc_final: 0.7694 (t0) REVERT: D 229 MET cc_start: 0.8301 (mmm) cc_final: 0.7959 (mmt) REVERT: D 230 LEU cc_start: 0.8522 (mt) cc_final: 0.8260 (tp) REVERT: D 250 GLU cc_start: 0.7868 (tp30) cc_final: 0.7597 (tt0) REVERT: D 262 LYS cc_start: 0.7955 (pttt) cc_final: 0.7753 (ptmt) REVERT: E 159 ASP cc_start: 0.7889 (m-30) cc_final: 0.6927 (m-30) REVERT: E 181 LYS cc_start: 0.8098 (mttt) cc_final: 0.7694 (mtmt) REVERT: F 159 ASP cc_start: 0.7425 (m-30) cc_final: 0.6917 (m-30) REVERT: F 191 ARG cc_start: 0.8216 (ttt90) cc_final: 0.7924 (ttt90) REVERT: F 255 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8353 (m) REVERT: F 264 ASP cc_start: 0.7395 (p0) cc_final: 0.6823 (t0) REVERT: G 62 SER cc_start: 0.8321 (t) cc_final: 0.8104 (m) REVERT: G 123 SER cc_start: 0.7446 (OUTLIER) cc_final: 0.7194 (m) REVERT: G 231 ARG cc_start: 0.7476 (ttm110) cc_final: 0.6970 (ttp80) REVERT: H 163 ASP cc_start: 0.8107 (m-30) cc_final: 0.7632 (m-30) REVERT: H 203 ASP cc_start: 0.7926 (t0) cc_final: 0.7652 (t0) REVERT: h 577 GLN cc_start: 0.6856 (tt0) cc_final: 0.6544 (tm-30) REVERT: h 581 GLU cc_start: 0.5930 (mt-10) cc_final: 0.5075 (mt-10) REVERT: I 223 ASN cc_start: 0.6844 (m110) cc_final: 0.6377 (m-40) REVERT: I 238 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7838 (mt-10) REVERT: J 20 TRP cc_start: 0.7144 (t60) cc_final: 0.6870 (t60) REVERT: J 85 ARG cc_start: 0.6498 (mmt90) cc_final: 0.5898 (mtp180) REVERT: J 160 ILE cc_start: 0.8630 (mt) cc_final: 0.8191 (mm) outliers start: 34 outliers final: 20 residues processed: 364 average time/residue: 0.4064 time to fit residues: 218.3267 Evaluate side-chains 336 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 313 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 211 TRP 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 572 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 210 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 232 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 206 ASN F 206 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 = 0.3615 r_free = 0.3615 target = 0.141159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.107995 restraints weight = 30041.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109096 restraints weight = 32182.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109980 restraints weight = 27261.209| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5345 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= 0.112 Angle : 0.491 8.422 31799 Z= 0.259 Chirality : 0.040 0.185 3531 Planarity : 0.003 0.035 3858 Dihedral : 16.205 179.772 3794 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.82 % Allowed : 13.17 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.16), residues: 2670 helix: 2.04 (0.13), residues: 1620 sheet: 1.97 (0.27), residues: 280 loop : 0.14 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 20 HIS 0.003 0.001 HIS G 77 PHE 0.007 0.001 PHE C 125 TYR 0.009 0.001 TYR F 115 ARG 0.007 0.000 ARG d 579 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 1147) hydrogen bonds : angle 4.20399 ( 3285) covalent geometry : bond 0.00252 (23487) covalent geometry : angle 0.49075 (31799) Misc. bond : bond 0.00248 ( 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 375 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 332 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7798 (tttm) cc_final: 0.7199 (ttpt) REVERT: A 113 LEU cc_start: 0.8466 (mt) cc_final: 0.8059 (mt) REVERT: A 206 ASN cc_start: 0.8486 (m-40) cc_final: 0.8184 (m110) REVERT: B 211 TRP cc_start: 0.8648 (OUTLIER) cc_final: 0.8382 (t-100) REVERT: B 230 LEU cc_start: 0.8728 (mt) cc_final: 0.8374 (tp) REVERT: C 180 ILE cc_start: 0.8482 (tt) cc_final: 0.8044 (tt) REVERT: C 182 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.6724 (ttp-110) REVERT: C 230 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7960 (tp) REVERT: D 113 LEU cc_start: 0.8156 (mt) cc_final: 0.7809 (mt) REVERT: D 203 ASP cc_start: 0.7987 (t0) cc_final: 0.7629 (t0) REVERT: D 230 LEU cc_start: 0.8551 (mt) cc_final: 0.8266 (tp) REVERT: D 250 GLU cc_start: 0.7870 (tp30) cc_final: 0.7627 (tt0) REVERT: E 47 ASP cc_start: 0.7437 (m-30) cc_final: 0.7202 (m-30) REVERT: E 159 ASP cc_start: 0.7889 (m-30) cc_final: 0.6988 (m-30) REVERT: E 181 LYS cc_start: 0.8053 (mttt) cc_final: 0.7655 (mtmt) REVERT: F 22 GLN cc_start: 0.7225 (mm110) cc_final: 0.7022 (mm-40) REVERT: F 159 ASP cc_start: 0.7383 (m-30) cc_final: 0.6885 (m-30) REVERT: F 191 ARG cc_start: 0.8247 (ttt90) cc_final: 0.7945 (ttt90) REVERT: F 255 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8317 (m) REVERT: F 264 ASP cc_start: 0.7494 (p0) cc_final: 0.7061 (t0) REVERT: G 62 SER cc_start: 0.8374 (t) cc_final: 0.8167 (m) REVERT: G 119 LYS cc_start: 0.7058 (tptt) cc_final: 0.6224 (tptm) REVERT: G 123 SER cc_start: 0.7312 (OUTLIER) cc_final: 0.7067 (m) REVERT: G 231 ARG cc_start: 0.7498 (ttm110) cc_final: 0.6954 (ttp80) REVERT: H 163 ASP cc_start: 0.8135 (m-30) cc_final: 0.7628 (m-30) REVERT: H 203 ASP cc_start: 0.7958 (t0) cc_final: 0.7679 (t0) REVERT: H 231 ARG cc_start: 0.7811 (tpp80) cc_final: 0.7339 (mmt90) REVERT: h 577 GLN cc_start: 0.6901 (tt0) cc_final: 0.6682 (tm-30) REVERT: I 223 ASN cc_start: 0.6950 (m110) cc_final: 0.6590 (m-40) REVERT: I 225 LYS cc_start: 0.7171 (tptt) cc_final: 0.6743 (ptpp) REVERT: I 238 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7820 (mt-10) REVERT: i 579 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7275 (mtt90) REVERT: J 20 TRP cc_start: 0.7192 (t60) cc_final: 0.6943 (t60) REVERT: J 81 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6367 (mt0) REVERT: J 85 ARG cc_start: 0.6298 (mmt90) cc_final: 0.5868 (mtp180) REVERT: J 160 ILE cc_start: 0.8576 (mt) cc_final: 0.8185 (mm) outliers start: 43 outliers final: 27 residues processed: 361 average time/residue: 0.4079 time to fit residues: 217.3813 Evaluate side-chains 347 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 315 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 89 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 211 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 230 LEU 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 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 G residue 64 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 28 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 152 optimal weight: 0.0470 chunk 234 optimal weight: 8.9990 chunk 243 optimal weight: 0.8980 chunk 235 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 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 = 0.3629 r_free = 0.3629 target = 0.142370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109378 restraints weight = 30063.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110500 restraints weight = 31679.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.111273 restraints weight = 27772.634| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23496 Z= 0.097 Angle : 0.473 8.279 31799 Z= 0.251 Chirality : 0.039 0.179 3531 Planarity : 0.003 0.034 3858 Dihedral : 16.023 177.587 3794 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.60 % Allowed : 14.14 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.16), residues: 2670 helix: 2.09 (0.13), residues: 1630 sheet: 1.93 (0.27), residues: 280 loop : 0.25 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 211 HIS 0.002 0.000 HIS I 77 PHE 0.004 0.001 PHE D 125 TYR 0.006 0.001 TYR F 93 ARG 0.007 0.000 ARG d 579 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 1147) hydrogen bonds : angle 4.17854 ( 3285) covalent geometry : bond 0.00211 (23487) covalent geometry : angle 0.47327 (31799) Misc. bond : bond 0.00210 ( 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 376 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 338 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6773 (tt) REVERT: A 107 LYS cc_start: 0.7933 (tttm) cc_final: 0.7213 (ttpt) REVERT: A 113 LEU cc_start: 0.8424 (mt) cc_final: 0.8033 (mt) REVERT: A 127 ASP cc_start: 0.6900 (m-30) cc_final: 0.6456 (m-30) REVERT: B 211 TRP cc_start: 0.8626 (t-100) cc_final: 0.8390 (t-100) REVERT: B 230 LEU cc_start: 0.8509 (mt) cc_final: 0.8280 (tp) REVERT: C 180 ILE cc_start: 0.8476 (tt) cc_final: 0.8024 (tt) REVERT: C 182 ARG cc_start: 0.7338 (ttm-80) cc_final: 0.6716 (ttp-110) REVERT: C 230 LEU cc_start: 0.8219 (mt) cc_final: 0.7967 (tp) REVERT: D 113 LEU cc_start: 0.8083 (mt) cc_final: 0.7768 (mt) REVERT: D 203 ASP cc_start: 0.7945 (t0) cc_final: 0.7675 (t0) REVERT: D 250 GLU cc_start: 0.7865 (tp30) cc_final: 0.7612 (tt0) REVERT: E 47 ASP cc_start: 0.7352 (m-30) cc_final: 0.7107 (m-30) REVERT: E 159 ASP cc_start: 0.7755 (m-30) cc_final: 0.6990 (m-30) REVERT: E 181 LYS cc_start: 0.7950 (mttt) cc_final: 0.7460 (mtmt) REVERT: F 89 VAL cc_start: 0.9202 (t) cc_final: 0.8933 (m) REVERT: F 159 ASP cc_start: 0.7350 (m-30) cc_final: 0.6847 (m-30) REVERT: F 191 ARG cc_start: 0.8215 (ttt90) cc_final: 0.7918 (ttt90) REVERT: F 225 LYS cc_start: 0.7739 (pttt) cc_final: 0.7430 (pptt) REVERT: F 255 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8355 (m) REVERT: F 264 ASP cc_start: 0.7579 (p0) cc_final: 0.7112 (t0) REVERT: G 119 LYS cc_start: 0.7067 (tptt) cc_final: 0.6101 (tptm) REVERT: G 123 SER cc_start: 0.7285 (OUTLIER) cc_final: 0.7050 (m) REVERT: G 231 ARG cc_start: 0.7483 (ttm110) cc_final: 0.6946 (ttp80) REVERT: H 163 ASP cc_start: 0.7995 (m-30) cc_final: 0.7447 (m-30) REVERT: h 577 GLN cc_start: 0.6889 (tt0) cc_final: 0.6681 (tm-30) REVERT: I 238 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7825 (mt-10) REVERT: I 261 LYS cc_start: 0.7273 (mmtt) cc_final: 0.6928 (mmtm) REVERT: J 20 TRP cc_start: 0.7179 (t60) cc_final: 0.6919 (t60) REVERT: J 81 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6369 (mt0) REVERT: J 160 ILE cc_start: 0.8540 (mt) cc_final: 0.8163 (mm) REVERT: J 214 MET cc_start: 0.6109 (mmp) cc_final: 0.5905 (mmt) outliers start: 38 outliers final: 26 residues processed: 367 average time/residue: 0.3825 time to fit residues: 210.6614 Evaluate side-chains 344 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 314 time to evaluate : 2.598 ------------------------------------------------------------------------------- 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 89 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 255 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 28 LEU 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 222 SER Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 152 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 92 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 221 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 246 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 169 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108183 restraints weight = 29984.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109853 restraints weight = 33429.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110664 restraints weight = 25255.617| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23496 Z= 0.103 Angle : 0.482 7.488 31799 Z= 0.254 Chirality : 0.040 0.176 3531 Planarity : 0.003 0.034 3858 Dihedral : 15.932 178.051 3794 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.86 % Allowed : 13.97 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.16), residues: 2670 helix: 2.13 (0.13), residues: 1620 sheet: 1.91 (0.26), residues: 280 loop : 0.29 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 211 HIS 0.002 0.000 HIS G 77 PHE 0.005 0.001 PHE H 190 TYR 0.008 0.001 TYR j 575 ARG 0.008 0.000 ARG j 579 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 1147) hydrogen bonds : angle 4.18679 ( 3285) covalent geometry : bond 0.00228 (23487) covalent geometry : angle 0.48185 (31799) Misc. bond : bond 0.00227 ( 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 363 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 319 time to evaluate : 2.746 Fit side-chains REVERT: A 21 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6796 (tt) REVERT: A 107 LYS cc_start: 0.7850 (tttm) cc_final: 0.7271 (ttpt) REVERT: A 113 LEU cc_start: 0.8446 (mt) cc_final: 0.8049 (mt) REVERT: A 205 LYS cc_start: 0.8547 (tmmt) cc_final: 0.8231 (tptp) REVERT: A 206 ASN cc_start: 0.8547 (m-40) cc_final: 0.8303 (m110) REVERT: B 211 TRP cc_start: 0.8633 (OUTLIER) cc_final: 0.8395 (t-100) REVERT: B 230 LEU cc_start: 0.8687 (mt) cc_final: 0.8262 (tp) REVERT: C 180 ILE cc_start: 0.8522 (tt) cc_final: 0.8157 (tt) REVERT: C 182 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.6712 (ttp-110) REVERT: C 230 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7987 (tp) REVERT: D 113 LEU cc_start: 0.8062 (mt) cc_final: 0.7678 (mt) REVERT: D 203 ASP cc_start: 0.7921 (t0) cc_final: 0.7690 (t0) REVERT: D 250 GLU cc_start: 0.7796 (tp30) cc_final: 0.7549 (mt-10) REVERT: E 47 ASP cc_start: 0.7397 (m-30) cc_final: 0.7148 (m-30) REVERT: E 159 ASP cc_start: 0.7780 (m-30) cc_final: 0.7005 (m-30) REVERT: F 89 VAL cc_start: 0.9216 (t) cc_final: 0.8957 (m) REVERT: F 159 ASP cc_start: 0.7336 (m-30) cc_final: 0.7035 (m-30) REVERT: F 191 ARG cc_start: 0.8244 (ttt90) cc_final: 0.7937 (ttt90) REVERT: F 225 LYS cc_start: 0.7745 (pttt) cc_final: 0.7394 (pptt) REVERT: F 264 ASP cc_start: 0.7581 (p0) cc_final: 0.7230 (t0) REVERT: G 231 ARG cc_start: 0.7507 (ttm110) cc_final: 0.6967 (ttp80) REVERT: H 163 ASP cc_start: 0.7980 (m-30) cc_final: 0.7447 (m-30) REVERT: H 231 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7276 (mmt90) REVERT: h 577 GLN cc_start: 0.6879 (tt0) cc_final: 0.6596 (tm-30) REVERT: h 581 GLU cc_start: 0.5827 (mt-10) cc_final: 0.4969 (mt-10) REVERT: I 140 MET cc_start: 0.9101 (ttp) cc_final: 0.8859 (ttp) REVERT: I 238 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7799 (mt-10) REVERT: I 261 LYS cc_start: 0.7430 (mmtt) cc_final: 0.7153 (mmtm) REVERT: i 579 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7212 (mtt90) REVERT: J 20 TRP cc_start: 0.7203 (t60) cc_final: 0.6963 (t60) REVERT: J 81 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6551 (mt0) REVERT: J 140 MET cc_start: 0.9226 (ttp) cc_final: 0.8936 (ttm) REVERT: J 160 ILE cc_start: 0.8567 (mt) cc_final: 0.8192 (mm) REVERT: J 214 MET cc_start: 0.6433 (mmp) cc_final: 0.6208 (mmt) outliers start: 44 outliers final: 30 residues processed: 351 average time/residue: 0.3912 time to fit residues: 204.8812 Evaluate side-chains 342 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 308 time to evaluate : 2.828 ------------------------------------------------------------------------------- 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 89 VAL Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 123 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 261 LYS 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 I residue 25 ILE Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 152 GLU Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.1278 > 50: distance: 24 - 28: 17.928 distance: 28 - 29: 10.810 distance: 29 - 30: 8.684 distance: 29 - 32: 14.965 distance: 30 - 31: 7.683 distance: 30 - 36: 10.567 distance: 32 - 33: 12.661 distance: 33 - 34: 18.582 distance: 33 - 35: 8.045 distance: 36 - 37: 10.548 distance: 36 - 42: 8.005 distance: 37 - 38: 6.622 distance: 37 - 40: 28.339 distance: 38 - 39: 18.285 distance: 38 - 43: 12.080 distance: 40 - 41: 44.643 distance: 41 - 42: 18.901 distance: 43 - 44: 17.817 distance: 44 - 45: 34.005 distance: 44 - 47: 33.820 distance: 45 - 46: 25.492 distance: 45 - 50: 30.014 distance: 47 - 48: 24.604 distance: 47 - 49: 35.448 distance: 50 - 51: 42.052 distance: 51 - 52: 11.986 distance: 51 - 54: 12.800 distance: 52 - 53: 20.870 distance: 52 - 56: 18.377 distance: 54 - 55: 27.802 distance: 56 - 57: 16.688 distance: 57 - 58: 7.261 distance: 57 - 60: 18.395 distance: 58 - 59: 19.591 distance: 58 - 62: 28.180 distance: 60 - 61: 24.144 distance: 62 - 63: 15.174 distance: 63 - 64: 28.218 distance: 63 - 66: 7.813 distance: 64 - 65: 46.379 distance: 64 - 70: 11.423 distance: 66 - 67: 33.399 distance: 67 - 68: 14.692 distance: 67 - 69: 26.311 distance: 70 - 71: 14.906 distance: 71 - 72: 21.412 distance: 71 - 74: 37.911 distance: 72 - 73: 46.815 distance: 72 - 78: 39.495 distance: 74 - 75: 15.014 distance: 75 - 76: 29.718 distance: 75 - 77: 47.649 distance: 78 - 79: 23.126 distance: 79 - 80: 6.739 distance: 79 - 82: 18.039 distance: 80 - 81: 8.932 distance: 80 - 87: 5.335 distance: 82 - 83: 13.115 distance: 83 - 84: 20.195 distance: 84 - 85: 10.825 distance: 85 - 86: 32.641 distance: 88 - 89: 16.150 distance: 88 - 91: 17.693 distance: 89 - 90: 6.225 distance: 89 - 93: 8.946 distance: 90 - 119: 11.814 distance: 91 - 92: 9.148 distance: 93 - 94: 6.311 distance: 94 - 95: 6.634 distance: 94 - 97: 8.381 distance: 95 - 96: 8.040 distance: 95 - 102: 6.613 distance: 96 - 127: 9.176 distance: 97 - 98: 7.032 distance: 98 - 99: 12.274 distance: 99 - 100: 5.741 distance: 100 - 101: 10.489