Starting phenix.real_space_refine on Thu May 22 13:47:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7svv_25454/05_2025/7svv_25454.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svv_25454/05_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_25454/05_2025/7svv_25454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svv_25454/05_2025/7svv_25454.map" model { file = "/net/cci-nas-00/data/ceres_data/7svv_25454/05_2025/7svv_25454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svv_25454/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 12.63, per 1000 atoms: 0.55 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: 6.22 Conformation dependent library (CDL) restraints added in 2.9 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: 6.65 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: 7.27 Time building geometry restraints manager: 7.13 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: 0.740 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: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 52.850 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.120 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.850 ------------------------------------------------------------------------------- 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 : 2.617 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: 0.4887 time to fit residues: 482.3915 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 : 2.481 ------------------------------------------------------------------------------- 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 = 30123.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116561 restraints weight = 32830.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117687 restraints weight = 26891.516| |-----------------------------------------------------------------------------| 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 : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7435 (tttm) cc_final: 0.6888 (ttpt) REVERT: A 113 LEU cc_start: 0.8573 (mt) cc_final: 0.7911 (mt) REVERT: A 127 ASP cc_start: 0.6974 (m-30) cc_final: 0.6609 (m-30) REVERT: A 203 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7826 (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: 0.6826 (pm20) cc_final: 0.6612 (pm20) REVERT: C 153 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7906 (t) REVERT: C 182 ARG cc_start: 0.7146 (ttm-80) cc_final: 0.6581 (ttp-110) REVERT: C 230 LEU cc_start: 0.8163 (mt) cc_final: 0.7947 (tp) REVERT: D 113 LEU cc_start: 0.8369 (mt) cc_final: 0.8148 (mt) REVERT: D 203 ASP cc_start: 0.7619 (t0) cc_final: 0.7267 (t0) REVERT: D 229 MET cc_start: 0.8171 (mmm) cc_final: 0.7889 (mmt) REVERT: D 230 LEU cc_start: 0.8662 (mt) cc_final: 0.8313 (tp) REVERT: D 250 GLU cc_start: 0.7894 (tp30) cc_final: 0.7514 (tt0) REVERT: E 181 LYS cc_start: 0.8199 (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: 0.7531 (m-30) cc_final: 0.7014 (m-30) REVERT: G 27 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7645 (ttp80) REVERT: G 33 ILE cc_start: 0.9017 (mt) cc_final: 0.8816 (mm) REVERT: G 54 LYS cc_start: 0.7892 (mmtm) cc_final: 0.7671 (mtpp) REVERT: G 76 ARG cc_start: 0.7393 (mtp180) cc_final: 0.6847 (mtp180) REVERT: G 113 LEU cc_start: 0.7691 (mt) cc_final: 0.7377 (mt) REVERT: G 159 ASP cc_start: 0.7719 (m-30) cc_final: 0.7474 (m-30) REVERT: G 231 ARG cc_start: 0.7165 (ttm110) cc_final: 0.6826 (ttp80) REVERT: H 159 ASP cc_start: 0.7392 (m-30) cc_final: 0.6887 (m-30) REVERT: H 163 ASP cc_start: 0.7996 (m-30) cc_final: 0.7735 (m-30) REVERT: H 203 ASP cc_start: 0.7904 (t0) cc_final: 0.7634 (t0) REVERT: I 206 ASN cc_start: 0.7807 (m-40) cc_final: 0.7600 (m-40) REVERT: I 238 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7777 (mt-10) REVERT: J 78 LYS cc_start: 0.7950 (mttt) cc_final: 0.7304 (mtpt) REVERT: J 261 LYS cc_start: 0.6275 (mmtt) cc_final: 0.5920 (ttpp) REVERT: J 269 GLN cc_start: 0.7588 (mt0) cc_final: 0.7229 (mt0) outliers start: 39 outliers final: 19 residues processed: 423 average time/residue: 0.4218 time to fit residues: 257.8932 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 : 2.457 ------------------------------------------------------------------------------- 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: 0.9990 chunk 29 optimal weight: 7.9990 chunk 167 optimal weight: 0.5980 chunk 204 optimal weight: 6.9990 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: 0.3980 chunk 160 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 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 = 0.145095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.111941 restraints weight = 30105.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112993 restraints weight = 31760.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114055 restraints weight = 26752.154| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4379 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= 0.102 Angle : 0.495 6.235 31799 Z= 0.263 Chirality : 0.040 0.215 3531 Planarity : 0.004 0.035 3858 Dihedral : 16.321 176.787 3794 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.18 % Allowed : 10.68 % 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 G 20 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 0.03246 ( 1147) hydrogen bonds : angle 4.27935 ( 3285) covalent geometry : bond 0.00215 (23487) covalent geometry : angle 0.49544 (31799) Misc. bond : bond 0.00261 ( 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 394 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 366 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7452 (tttm) cc_final: 0.7083 (ttpt) REVERT: A 113 LEU cc_start: 0.8442 (mt) cc_final: 0.7940 (mt) REVERT: A 203 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7770 (t0) REVERT: A 205 LYS cc_start: 0.8365 (tmmt) cc_final: 0.8048 (tptp) REVERT: B 211 TRP cc_start: 0.8553 (t-100) cc_final: 0.8302 (t-100) REVERT: B 230 LEU cc_start: 0.8733 (mt) cc_final: 0.8483 (tp) REVERT: C 182 ARG cc_start: 0.7218 (ttm-80) cc_final: 0.6684 (ttp-110) REVERT: C 230 LEU cc_start: 0.8202 (mt) cc_final: 0.7988 (tp) REVERT: D 113 LEU cc_start: 0.8228 (mt) cc_final: 0.7921 (mt) REVERT: D 203 ASP cc_start: 0.7937 (t0) cc_final: 0.7560 (t0) REVERT: D 213 GLN cc_start: 0.8005 (mt0) cc_final: 0.7793 (mm-40) REVERT: D 229 MET cc_start: 0.8272 (mmm) cc_final: 0.7991 (mmt) REVERT: D 230 LEU cc_start: 0.8623 (mt) cc_final: 0.8277 (tp) REVERT: D 250 GLU cc_start: 0.7843 (tp30) cc_final: 0.7480 (tt0) REVERT: E 181 LYS cc_start: 0.8108 (mttt) cc_final: 0.7754 (mtmt) REVERT: F 159 ASP cc_start: 0.7493 (m-30) cc_final: 0.6981 (m-30) REVERT: F 191 ARG cc_start: 0.8211 (ttt90) cc_final: 0.7948 (ttt90) REVERT: F 255 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8325 (m) REVERT: G 27 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7508 (ttt-90) REVERT: G 214 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7155 (mtp) REVERT: G 231 ARG cc_start: 0.7310 (ttm110) cc_final: 0.6942 (ttp80) REVERT: G 255 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7420 (m) REVERT: G 269 GLN cc_start: 0.8001 (tp40) cc_final: 0.7751 (tp-100) REVERT: H 131 GLU cc_start: 0.6415 (tp30) cc_final: 0.5826 (tp30) REVERT: H 163 ASP cc_start: 0.8059 (m-30) cc_final: 0.7693 (m-30) REVERT: H 203 ASP cc_start: 0.7972 (t0) cc_final: 0.7712 (t0) REVERT: I 206 ASN cc_start: 0.7836 (m-40) cc_final: 0.7536 (m-40) REVERT: I 223 ASN cc_start: 0.6545 (m110) cc_final: 0.5884 (t0) REVERT: I 238 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7752 (mt-10) REVERT: J 223 ASN cc_start: 0.6797 (m-40) cc_final: 0.6392 (t0) REVERT: J 269 GLN cc_start: 0.7680 (mt0) cc_final: 0.7418 (mt0) outliers start: 28 outliers final: 13 residues processed: 380 average time/residue: 0.4110 time to fit residues: 225.9631 Evaluate side-chains 322 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 305 time to evaluate : 2.724 ------------------------------------------------------------------------------- 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 572 VAL Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain I residue 64 THR 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 54.7719 > 50: distance: 59 - 82: 5.449 distance: 66 - 90: 8.970 distance: 74 - 101: 4.533 distance: 77 - 82: 6.737 distance: 78 - 110: 6.842 distance: 82 - 83: 9.133 distance: 83 - 84: 6.486 distance: 83 - 86: 3.751 distance: 84 - 85: 3.828 distance: 84 - 90: 6.787 distance: 85 - 115: 15.434 distance: 86 - 87: 7.110 distance: 87 - 89: 7.969 distance: 90 - 91: 3.151 distance: 91 - 92: 6.530 distance: 92 - 93: 5.294 distance: 92 - 101: 4.999 distance: 93 - 120: 12.048 distance: 95 - 96: 5.877 distance: 98 - 99: 3.557 distance: 98 - 100: 4.216 distance: 102 - 105: 3.048 distance: 103 - 104: 5.119 distance: 103 - 110: 9.559 distance: 104 - 128: 9.541 distance: 105 - 106: 3.392 distance: 106 - 107: 4.204 distance: 107 - 108: 3.105 distance: 107 - 109: 4.242 distance: 110 - 111: 5.458 distance: 111 - 112: 11.272 distance: 111 - 114: 3.267 distance: 112 - 113: 15.260 distance: 112 - 115: 6.536 distance: 113 - 139: 20.200 distance: 115 - 116: 14.318 distance: 116 - 117: 13.477 distance: 116 - 119: 10.482 distance: 117 - 118: 14.946 distance: 117 - 120: 13.424 distance: 118 - 145: 29.437 distance: 120 - 121: 12.575 distance: 121 - 122: 4.246 distance: 121 - 124: 4.915 distance: 122 - 123: 6.845 distance: 122 - 128: 5.192 distance: 123 - 153: 22.871 distance: 124 - 125: 3.501 distance: 125 - 127: 8.556 distance: 128 - 129: 6.958 distance: 129 - 130: 9.269 distance: 129 - 132: 6.663 distance: 130 - 131: 15.744 distance: 130 - 139: 32.285 distance: 132 - 133: 5.919 distance: 133 - 134: 3.283 distance: 134 - 135: 3.407 distance: 139 - 140: 35.187 distance: 140 - 141: 20.318 distance: 140 - 143: 42.366 distance: 141 - 142: 12.854 distance: 141 - 145: 37.894 distance: 143 - 144: 28.893 distance: 145 - 146: 22.627 distance: 146 - 147: 34.443 distance: 146 - 149: 10.569 distance: 147 - 148: 10.417 distance: 147 - 153: 18.761 distance: 149 - 150: 22.455 distance: 150 - 151: 24.899 distance: 150 - 152: 31.349 distance: 153 - 154: 18.353 distance: 154 - 155: 14.561 distance: 154 - 157: 7.075 distance: 155 - 156: 19.760 distance: 155 - 159: 12.820 distance: 157 - 158: 32.188