Starting phenix.real_space_refine on Wed Jun 18 23:16:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iaw_4440/06_2025/6iaw_4440.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iaw_4440/06_2025/6iaw_4440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6iaw_4440/06_2025/6iaw_4440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iaw_4440/06_2025/6iaw_4440.map" model { file = "/net/cci-nas-00/data/ceres_data/6iaw_4440/06_2025/6iaw_4440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iaw_4440/06_2025/6iaw_4440.cif" } resolution = 3.8 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= 0.660 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 13949 2.51 5 N 3640 2.21 5 O 4267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21929 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3190 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 9, 'TRANS': 383} Chain: "B" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "C" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "J" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "I" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "D" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 237 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "H" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Chain: "M" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2738 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 8, 'TRANS': 329} Chain: "N" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "O" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "Q" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "S" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "L" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Chain: "X" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "Y" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 79 Classifications: {'peptide': 16} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 15} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 54 Classifications: {'peptide': 12} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 6} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 13.13, per 1000 atoms: 0.60 Number of scatterers: 21929 At special positions: 0 Unit cell: (189.214, 159.45, 120.119, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 4267 8.00 N 3640 7.00 C 13949 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=0, symmetry=0 Time building additional restraints: 5.07 Conformation dependent library (CDL) restraints added in 2.9 seconds 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5322 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 33 sheets defined 26.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 17 through 21 removed outlier: 6.310A pdb=" N ALA A 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 removed outlier: 4.053A pdb=" N HIS A 27 " --> pdb=" O GLN A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.582A pdb=" N LEU A 107 " --> pdb=" O ASN A 104 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 108 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.556A pdb=" N ASN A 141 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.791A pdb=" N ALA A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 182 Processing helix chain 'A' and resid 195 through 205 removed outlier: 4.544A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.883A pdb=" N ARG A 220 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 removed outlier: 5.608A pdb=" N ILE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.635A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 removed outlier: 4.153A pdb=" N HIS B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 104 through 110 removed outlier: 4.046A pdb=" N MET B 108 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.771A pdb=" N PHE B 142 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 182 removed outlier: 3.580A pdb=" N TYR B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.690A pdb=" N SER B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 4.269A pdb=" N ALA B 225 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 226 " --> pdb=" O GLY B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 226' Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.505A pdb=" N LYS B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.585A pdb=" N ALA B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 16 Processing helix chain 'C' and resid 22 through 27 removed outlier: 4.138A pdb=" N HIS C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.017A pdb=" N LEU C 107 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 145 through 180 removed outlier: 5.076A pdb=" N ILE C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 243 through 257 removed outlier: 5.655A pdb=" N ILE C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 268 removed outlier: 4.181A pdb=" N ASP C 268 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 290 through 299 Processing helix chain 'E' and resid 13 through 17 Processing helix chain 'H' and resid 38 through 53 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 104 through 110 removed outlier: 3.501A pdb=" N LEU M 107 " --> pdb=" O ASN M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 141 removed outlier: 3.890A pdb=" N ASN M 141 " --> pdb=" O ASP M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 182 removed outlier: 3.649A pdb=" N TYR M 156 " --> pdb=" O ALA M 152 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE M 163 " --> pdb=" O LYS M 159 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN M 164 " --> pdb=" O ILE M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 205 removed outlier: 3.513A pdb=" N ILE M 205 " --> pdb=" O VAL M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 221 Processing helix chain 'M' and resid 244 through 258 removed outlier: 5.831A pdb=" N ILE M 255 " --> pdb=" O LEU M 251 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ALA M 256 " --> pdb=" O ASP M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 268 removed outlier: 4.138A pdb=" N ASP M 268 " --> pdb=" O ASP M 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 265 through 268' Processing helix chain 'M' and resid 290 through 299 removed outlier: 3.620A pdb=" N ALA M 299 " --> pdb=" O ASP M 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 76 Processing helix chain 'N' and resid 104 through 110 removed outlier: 3.630A pdb=" N LEU N 107 " --> pdb=" O ASN N 104 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS N 110 " --> pdb=" O LEU N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 142 removed outlier: 3.798A pdb=" N PHE N 142 " --> pdb=" O ARG N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 182 removed outlier: 3.969A pdb=" N TYR N 156 " --> pdb=" O ALA N 152 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE N 163 " --> pdb=" O LYS N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 209 removed outlier: 3.700A pdb=" N SER N 199 " --> pdb=" O GLU N 195 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU N 206 " --> pdb=" O PHE N 202 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN N 209 " --> pdb=" O ILE N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 217 through 221 Processing helix chain 'N' and resid 243 through 253 Processing helix chain 'N' and resid 266 through 268 No H-bonds generated for 'chain 'N' and resid 266 through 268' Processing helix chain 'N' and resid 290 through 299 removed outlier: 3.560A pdb=" N ALA N 299 " --> pdb=" O ASP N 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 20 removed outlier: 3.870A pdb=" N LYS O 19 " --> pdb=" O LYS O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 27 removed outlier: 3.603A pdb=" N ASN O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS O 27 " --> pdb=" O GLN O 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 22 through 27' Processing helix chain 'O' and resid 72 through 76 Processing helix chain 'O' and resid 106 through 110 Processing helix chain 'O' and resid 137 through 141 Processing helix chain 'O' and resid 145 through 180 removed outlier: 3.633A pdb=" N THR O 149 " --> pdb=" O LEU O 145 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE O 163 " --> pdb=" O LYS O 159 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN O 164 " --> pdb=" O ILE O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 205 Processing helix chain 'O' and resid 217 through 221 Processing helix chain 'O' and resid 244 through 253 Processing helix chain 'O' and resid 266 through 268 No H-bonds generated for 'chain 'O' and resid 266 through 268' Processing helix chain 'O' and resid 290 through 300 removed outlier: 3.704A pdb=" N TYR O 300 " --> pdb=" O PHE O 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 53 Processing helix chain 'X' and resid 121 through 129 removed outlier: 3.584A pdb=" N UNK X 125 " --> pdb=" O UNK X 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 53 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.664A pdb=" N GLU A 88 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N TYR A 85 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR C 61 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU A 87 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 355 Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 355 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 190 removed outlier: 5.865A pdb=" N ARG A 189 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE A 271 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A 240 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N PHE A 273 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 242 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 279 through 282 removed outlier: 4.807A pdb=" N VAL A 279 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 61 removed outlier: 7.557A pdb=" N GLU O 87 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR B 61 " --> pdb=" O GLU O 87 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 78 removed outlier: 6.056A pdb=" N LYS B 77 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 91 Processing sheet with id=AB1, first strand: chain 'B' and resid 188 through 190 removed outlier: 3.545A pdb=" N THR B 394 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE B 271 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 240 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 280 through 282 Processing sheet with id=AB3, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.841A pdb=" N PHE B 286 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 86 through 88 Processing sheet with id=AB5, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'C' and resid 189 through 190 removed outlier: 3.612A pdb=" N ILE C 271 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 280 through 282 Processing sheet with id=AB8, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AB9, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AC1, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AC2, first strand: chain 'M' and resid 77 through 78 removed outlier: 3.587A pdb=" N LYS M 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 87 through 91 Processing sheet with id=AC4, first strand: chain 'M' and resid 188 through 190 removed outlier: 5.287A pdb=" N ARG M 189 " --> pdb=" O THR M 394 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TYR M 341 " --> pdb=" O THR M 243 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR M 243 " --> pdb=" O TYR M 341 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 279 through 282 removed outlier: 4.665A pdb=" N VAL M 279 " --> pdb=" O ILE M 334 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 86 through 91 removed outlier: 3.587A pdb=" N GLU N 88 " --> pdb=" O LYS N 119 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 188 through 190 removed outlier: 3.615A pdb=" N THR N 394 " --> pdb=" O ARG N 189 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 240 through 241 removed outlier: 6.687A pdb=" N ILE N 240 " --> pdb=" O ILE N 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'N' and resid 280 through 282 Processing sheet with id=AD1, first strand: chain 'N' and resid 286 through 287 removed outlier: 3.642A pdb=" N PHE N 286 " --> pdb=" O ILE N 311 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 77 through 78 removed outlier: 5.951A pdb=" N LYS O 77 " --> pdb=" O ARG O 354 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE O 131 " --> pdb=" O HIS O 374 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 189 through 190 removed outlier: 3.563A pdb=" N THR O 394 " --> pdb=" O ARG O 189 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE O 271 " --> pdb=" O ILE O 238 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE O 240 " --> pdb=" O ILE O 271 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE O 273 " --> pdb=" O ILE O 240 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR O 242 " --> pdb=" O PHE O 273 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 280 through 282 Processing sheet with id=AD5, first strand: chain 'L' and resid 21 through 23 Processing sheet with id=AD6, first strand: chain 'K' and resid 21 through 23 641 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.66 Time building geometry restraints manager: 6.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6956 1.34 - 1.46: 4786 1.46 - 1.58: 10446 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 22334 Sorted by residual: bond pdb=" CG GLU M 168 " pdb=" CD GLU M 168 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.33e+00 bond pdb=" CA ASN A 348 " pdb=" CB ASN A 348 " ideal model delta sigma weight residual 1.532 1.565 -0.032 1.56e-02 4.11e+03 4.24e+00 bond pdb=" CA SER S 14 " pdb=" C SER S 14 " ideal model delta sigma weight residual 1.521 1.548 -0.027 1.38e-02 5.25e+03 3.94e+00 bond pdb=" CA ILE S 45 " pdb=" CB ILE S 45 " ideal model delta sigma weight residual 1.540 1.567 -0.027 1.36e-02 5.41e+03 3.84e+00 bond pdb=" CG1 ILE M 91 " pdb=" CD1 ILE M 91 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.82e+00 ... (remaining 22329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 29545 3.71 - 7.43: 536 7.43 - 11.14: 70 11.14 - 14.85: 8 14.85 - 18.57: 4 Bond angle restraints: 30163 Sorted by residual: angle pdb=" N SER E 40 " pdb=" CA SER E 40 " pdb=" C SER E 40 " ideal model delta sigma weight residual 107.23 120.29 -13.06 1.67e+00 3.59e-01 6.11e+01 angle pdb=" N GLU C 326 " pdb=" CA GLU C 326 " pdb=" C GLU C 326 " ideal model delta sigma weight residual 111.71 117.97 -6.26 1.15e+00 7.56e-01 2.96e+01 angle pdb=" CG1 ILE I 45 " pdb=" CB ILE I 45 " pdb=" CG2 ILE I 45 " ideal model delta sigma weight residual 110.70 94.48 16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" C GLN S 44 " pdb=" N ILE S 45 " pdb=" CA ILE S 45 " ideal model delta sigma weight residual 121.97 131.68 -9.71 1.80e+00 3.09e-01 2.91e+01 angle pdb=" CA LEU B 183 " pdb=" CB LEU B 183 " pdb=" CG LEU B 183 " ideal model delta sigma weight residual 116.30 134.87 -18.57 3.50e+00 8.16e-02 2.81e+01 ... (remaining 30158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.76: 11955 14.76 - 29.53: 1079 29.53 - 44.29: 349 44.29 - 59.05: 34 59.05 - 73.82: 11 Dihedral angle restraints: 13428 sinusoidal: 5201 harmonic: 8227 Sorted by residual: dihedral pdb=" CA GLN I 44 " pdb=" C GLN I 44 " pdb=" N ILE I 45 " pdb=" CA ILE I 45 " ideal model delta harmonic sigma weight residual 180.00 121.63 58.37 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA GLN S 44 " pdb=" C GLN S 44 " pdb=" N ILE S 45 " pdb=" CA ILE S 45 " ideal model delta harmonic sigma weight residual 180.00 133.29 46.71 0 5.00e+00 4.00e-02 8.73e+01 dihedral pdb=" CA LEU C 206 " pdb=" C LEU C 206 " pdb=" N ASN C 207 " pdb=" CA ASN C 207 " ideal model delta harmonic sigma weight residual 180.00 141.62 38.38 0 5.00e+00 4.00e-02 5.89e+01 ... (remaining 13425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2526 0.073 - 0.145: 715 0.145 - 0.218: 102 0.218 - 0.290: 23 0.290 - 0.363: 4 Chirality restraints: 3370 Sorted by residual: chirality pdb=" CB ILE E 45 " pdb=" CA ILE E 45 " pdb=" CG1 ILE E 45 " pdb=" CG2 ILE E 45 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB ILE D 32 " pdb=" CA ILE D 32 " pdb=" CG1 ILE D 32 " pdb=" CG2 ILE D 32 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE I 45 " pdb=" CA ILE I 45 " pdb=" CG1 ILE I 45 " pdb=" CG2 ILE I 45 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 3367 not shown) Planarity restraints: 3876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN S 44 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C GLN S 44 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN S 44 " 0.028 2.00e-02 2.50e+03 pdb=" N ILE S 45 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 44 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C GLN I 44 " 0.068 2.00e-02 2.50e+03 pdb=" O GLN I 44 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE I 45 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU M 168 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" CD GLU M 168 " -0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU M 168 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU M 168 " 0.019 2.00e-02 2.50e+03 ... (remaining 3873 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 6 2.13 - 2.82: 7199 2.82 - 3.52: 30355 3.52 - 4.21: 51276 4.21 - 4.90: 84362 Nonbonded interactions: 173198 Sorted by model distance: nonbonded pdb=" OD2 ASP N 265 " pdb=" CD1 TYR Q 41 " model vdw 1.440 3.340 nonbonded pdb=" OD2 ASP M 265 " pdb=" CD1 TYR S 41 " model vdw 1.454 3.340 nonbonded pdb=" CG2 ILE B 261 " pdb=" OD1 ASP B 265 " model vdw 1.571 3.460 nonbonded pdb=" OD2 ASP B 265 " pdb=" CD1 TYR J 41 " model vdw 1.648 3.340 nonbonded pdb=" CG2 ILE A 261 " pdb=" OD1 ASP A 265 " model vdw 1.886 3.460 ... (remaining 173193 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' and resid 59 through 396) selection = (chain 'B' and resid 59 through 396) selection = (chain 'C' and resid 59 through 396) selection = chain 'M' selection = (chain 'N' and resid 59 through 396) selection = (chain 'O' and resid 59 through 396) } ncs_group { reference = chain 'E' selection = (chain 'I' and resid 1 through 54) selection = (chain 'J' and resid 1 through 54) selection = (chain 'Q' and resid 1 through 54) selection = (chain 'S' and resid 1 through 54) } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'X' and (resid 115 through 129 or (resid 130 and (name N or name CA or na \ me C or name O )))) selection = chain 'Y' } 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: 0.530 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: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 48.340 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.008 0.076 22334 Z= 0.374 Angle : 1.266 18.566 30163 Z= 0.667 Chirality : 0.067 0.363 3370 Planarity : 0.006 0.055 3876 Dihedral : 12.853 73.818 8106 Min Nonbonded Distance : 1.440 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.70 % Favored : 88.10 % Rotamer: Outliers : 1.42 % Allowed : 10.84 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -4.49 (0.13), residues: 2555 helix: -3.11 (0.16), residues: 519 sheet: -2.88 (0.20), residues: 455 loop : -3.10 (0.13), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 74 HIS 0.019 0.003 HIS S 46 PHE 0.025 0.003 PHE N 343 TYR 0.023 0.003 TYR N 121 ARG 0.017 0.001 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.16314 ( 627) hydrogen bonds : angle 7.82229 ( 1665) covalent geometry : bond 0.00781 (22334) covalent geometry : angle 1.26605 (30163) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 832 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8585 (pt0) cc_final: 0.7567 (mp10) REVERT: A 110 LYS cc_start: 0.7472 (mmpt) cc_final: 0.7188 (mmmt) REVERT: A 127 LYS cc_start: 0.9568 (mptm) cc_final: 0.9206 (mmmm) REVERT: A 163 ILE cc_start: 0.9369 (pp) cc_final: 0.9115 (pt) REVERT: A 174 MET cc_start: 0.7074 (mmp) cc_final: 0.6643 (mmm) REVERT: A 194 LYS cc_start: 0.9142 (tmmt) cc_final: 0.8752 (tptt) REVERT: A 203 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8853 (mt-10) REVERT: A 238 ILE cc_start: 0.9235 (pp) cc_final: 0.9003 (mp) REVERT: A 275 ASP cc_start: 0.8835 (t70) cc_final: 0.8525 (t0) REVERT: A 357 LYS cc_start: 0.9465 (mtpp) cc_final: 0.9062 (mtpp) REVERT: B 94 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8867 (p) REVERT: B 99 MET cc_start: 0.8223 (ppp) cc_final: 0.7656 (tmm) REVERT: B 127 LYS cc_start: 0.9238 (mtpp) cc_final: 0.8630 (mmmm) REVERT: B 139 ARG cc_start: 0.8526 (mmt90) cc_final: 0.8159 (mtp-110) REVERT: B 153 LEU cc_start: 0.8712 (tt) cc_final: 0.8419 (tt) REVERT: B 170 GLU cc_start: 0.9029 (pp20) cc_final: 0.8765 (pp20) REVERT: B 172 ARG cc_start: 0.8990 (ppt-90) cc_final: 0.8539 (ptt90) REVERT: B 220 ARG cc_start: 0.8499 (ttm110) cc_final: 0.8209 (mtm-85) REVERT: B 238 ILE cc_start: 0.9516 (pp) cc_final: 0.9252 (mp) REVERT: B 320 ASP cc_start: 0.8821 (t0) cc_final: 0.8482 (t0) REVERT: C 45 MET cc_start: 0.7919 (mpm) cc_final: 0.7570 (mpp) REVERT: C 94 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8377 (p) REVERT: C 99 MET cc_start: 0.8372 (pmm) cc_final: 0.8164 (pmm) REVERT: C 123 ASN cc_start: 0.9251 (p0) cc_final: 0.8957 (p0) REVERT: C 170 GLU cc_start: 0.8600 (pp20) cc_final: 0.8229 (pp20) REVERT: C 172 ARG cc_start: 0.9310 (ttp80) cc_final: 0.8545 (ptt90) REVERT: C 174 MET cc_start: 0.6788 (mmp) cc_final: 0.6270 (mmp) REVERT: C 244 ASP cc_start: 0.8646 (t70) cc_final: 0.8072 (t0) REVERT: C 320 ASP cc_start: 0.8587 (t70) cc_final: 0.8294 (t70) REVERT: C 370 ASP cc_start: 0.8891 (t0) cc_final: 0.8540 (t70) REVERT: C 391 ILE cc_start: 0.9732 (OUTLIER) cc_final: 0.9489 (mm) REVERT: J 1 MET cc_start: 0.8144 (ttp) cc_final: 0.7762 (tmm) REVERT: J 23 ARG cc_start: 0.8120 (mpp-170) cc_final: 0.7709 (mpt180) REVERT: J 29 ASN cc_start: 0.7988 (t0) cc_final: 0.7571 (t0) REVERT: J 36 LYS cc_start: 0.8989 (tmmm) cc_final: 0.8743 (pttt) REVERT: J 39 ASP cc_start: 0.9038 (p0) cc_final: 0.8730 (p0) REVERT: I 5 ASN cc_start: 0.8800 (t0) cc_final: 0.8498 (t0) REVERT: I 7 MET cc_start: 0.7053 (mmm) cc_final: 0.6712 (mmm) REVERT: E 17 ASP cc_start: 0.8973 (m-30) cc_final: 0.8683 (m-30) REVERT: E 29 ASN cc_start: 0.8829 (m110) cc_final: 0.8574 (m-40) REVERT: M 63 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8899 (tm) REVERT: M 109 LEU cc_start: 0.9428 (mt) cc_final: 0.9141 (tt) REVERT: M 129 GLN cc_start: 0.8330 (tp40) cc_final: 0.7593 (tp-100) REVERT: M 159 LYS cc_start: 0.9527 (ttmp) cc_final: 0.9103 (tppt) REVERT: M 234 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8485 (mmmt) REVERT: M 236 LYS cc_start: 0.9130 (mtmp) cc_final: 0.8909 (mtmm) REVERT: M 268 ASP cc_start: 0.8399 (t0) cc_final: 0.8132 (t70) REVERT: M 289 GLN cc_start: 0.8831 (mp10) cc_final: 0.8456 (mp-120) REVERT: M 291 GLN cc_start: 0.9554 (tp-100) cc_final: 0.9015 (tp-100) REVERT: M 295 ASP cc_start: 0.9303 (p0) cc_final: 0.9005 (p0) REVERT: M 353 LYS cc_start: 0.9209 (mtpp) cc_final: 0.8821 (mtpp) REVERT: M 356 THR cc_start: 0.9267 (p) cc_final: 0.8917 (t) REVERT: M 357 LYS cc_start: 0.8898 (mptt) cc_final: 0.8665 (mmmm) REVERT: M 364 PHE cc_start: 0.9515 (t80) cc_final: 0.9224 (t80) REVERT: M 387 PHE cc_start: 0.9198 (m-80) cc_final: 0.8970 (m-80) REVERT: N 28 ASP cc_start: 0.8774 (p0) cc_final: 0.8563 (p0) REVERT: N 31 LYS cc_start: 0.9002 (tptt) cc_final: 0.8780 (mmtm) REVERT: N 45 MET cc_start: 0.8384 (pmm) cc_final: 0.8001 (mpp) REVERT: N 51 ASN cc_start: 0.9313 (m110) cc_final: 0.8938 (t0) REVERT: N 92 MET cc_start: 0.9290 (mmm) cc_final: 0.8916 (mmm) REVERT: N 94 THR cc_start: 0.9145 (p) cc_final: 0.8386 (p) REVERT: N 97 ILE cc_start: 0.9647 (tt) cc_final: 0.9276 (tp) REVERT: N 126 VAL cc_start: 0.9651 (p) cc_final: 0.9274 (p) REVERT: N 128 LYS cc_start: 0.9498 (mmmt) cc_final: 0.9294 (mmmt) REVERT: N 139 ARG cc_start: 0.8475 (mmt90) cc_final: 0.8078 (mtp-110) REVERT: N 147 ASP cc_start: 0.8920 (p0) cc_final: 0.8437 (p0) REVERT: N 156 TYR cc_start: 0.9244 (t80) cc_final: 0.8713 (t80) REVERT: N 159 LYS cc_start: 0.9215 (ptpt) cc_final: 0.8855 (ttpt) REVERT: N 172 ARG cc_start: 0.9159 (ppt-90) cc_final: 0.8953 (ptt-90) REVERT: N 217 GLU cc_start: 0.7691 (tp30) cc_final: 0.7463 (tp30) REVERT: N 228 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8552 (tm-30) REVERT: N 234 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8787 (mmmt) REVERT: N 237 ASP cc_start: 0.8643 (p0) cc_final: 0.7746 (p0) REVERT: N 281 LYS cc_start: 0.9239 (tptp) cc_final: 0.8760 (tptp) REVERT: N 291 GLN cc_start: 0.9176 (tp40) cc_final: 0.8326 (tm-30) REVERT: N 295 ASP cc_start: 0.9435 (p0) cc_final: 0.8679 (p0) REVERT: N 302 ASP cc_start: 0.8739 (t0) cc_final: 0.8369 (t70) REVERT: N 304 GLN cc_start: 0.8394 (pp30) cc_final: 0.8083 (pp30) REVERT: N 309 ASP cc_start: 0.7553 (m-30) cc_final: 0.7276 (m-30) REVERT: N 346 ASP cc_start: 0.8882 (p0) cc_final: 0.8506 (p0) REVERT: N 387 PHE cc_start: 0.8971 (m-10) cc_final: 0.8547 (m-10) REVERT: O 39 TRP cc_start: 0.9345 (t-100) cc_final: 0.9129 (t-100) REVERT: O 79 GLN cc_start: 0.8556 (mm110) cc_final: 0.8223 (mm110) REVERT: O 97 ILE cc_start: 0.9375 (pp) cc_final: 0.8851 (pp) REVERT: O 108 MET cc_start: 0.8542 (ptm) cc_final: 0.8043 (mtt) REVERT: O 167 GLU cc_start: 0.8475 (tp30) cc_final: 0.7966 (tp30) REVERT: O 203 GLU cc_start: 0.8792 (pp20) cc_final: 0.8471 (pp20) REVERT: O 236 LYS cc_start: 0.9145 (pttp) cc_final: 0.8915 (ptpt) REVERT: O 261 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.4733 (pp) REVERT: Q 20 LEU cc_start: 0.9085 (tt) cc_final: 0.8538 (tt) REVERT: Q 21 ASN cc_start: 0.8282 (t0) cc_final: 0.8026 (t0) REVERT: Q 23 ARG cc_start: 0.8263 (pmm150) cc_final: 0.8003 (pmt170) REVERT: Q 33 ASP cc_start: 0.8282 (t70) cc_final: 0.7945 (t70) REVERT: S 10 MET cc_start: 0.8315 (mpt) cc_final: 0.7812 (mmm) REVERT: S 14 SER cc_start: 0.6663 (m) cc_final: 0.5382 (m) REVERT: S 39 ASP cc_start: 0.8295 (p0) cc_final: 0.8051 (p0) REVERT: S 49 SER cc_start: 0.8937 (t) cc_final: 0.8655 (p) outliers start: 33 outliers final: 2 residues processed: 849 average time/residue: 0.3928 time to fit residues: 485.3261 Evaluate side-chains 594 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 587 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain O residue 261 ILE Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 377 HIS B 70 ASN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 129 GLN C 182 GLN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN C 260 GLN ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 5 ASN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 ASN N 219 HIS N 374 HIS O 27 HIS ** O 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN S 5 ASN S 46 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.072686 restraints weight = 72199.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074915 restraints weight = 39544.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076422 restraints weight = 25748.646| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22334 Z= 0.267 Angle : 0.902 11.370 30163 Z= 0.466 Chirality : 0.050 0.353 3370 Planarity : 0.005 0.063 3876 Dihedral : 7.725 43.772 2984 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.31 % Favored : 88.61 % Rotamer: Outliers : 4.65 % Allowed : 17.13 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.75 (0.15), residues: 2555 helix: -1.74 (0.20), residues: 514 sheet: -2.65 (0.20), residues: 463 loop : -2.82 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 74 HIS 0.009 0.002 HIS I 46 PHE 0.020 0.002 PHE A 131 TYR 0.035 0.002 TYR Q 41 ARG 0.009 0.001 ARG S 23 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 627) hydrogen bonds : angle 6.26621 ( 1665) covalent geometry : bond 0.00572 (22334) covalent geometry : angle 0.90249 (30163) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 602 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8633 (pt0) cc_final: 0.7629 (mp10) REVERT: A 110 LYS cc_start: 0.7839 (mmpt) cc_final: 0.7567 (mmmt) REVERT: A 127 LYS cc_start: 0.9531 (mptm) cc_final: 0.9150 (mmmm) REVERT: A 167 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: A 168 GLU cc_start: 0.9321 (tt0) cc_final: 0.8845 (tt0) REVERT: A 203 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8778 (mt-10) REVERT: A 275 ASP cc_start: 0.8713 (t70) cc_final: 0.8404 (t0) REVERT: A 347 ILE cc_start: 0.9062 (tp) cc_final: 0.8654 (pt) REVERT: A 357 LYS cc_start: 0.9413 (mtpp) cc_final: 0.9043 (mtpp) REVERT: A 375 TRP cc_start: 0.8840 (m-90) cc_final: 0.8493 (m-10) REVERT: A 378 TYR cc_start: 0.9478 (p90) cc_final: 0.9181 (p90) REVERT: B 39 TRP cc_start: 0.9540 (t-100) cc_final: 0.9201 (t-100) REVERT: B 99 MET cc_start: 0.8185 (ppp) cc_final: 0.7503 (tmm) REVERT: B 127 LYS cc_start: 0.9331 (mtpp) cc_final: 0.8943 (mmmm) REVERT: B 139 ARG cc_start: 0.8734 (mmt90) cc_final: 0.8321 (mtp-110) REVERT: B 167 GLU cc_start: 0.8862 (tp30) cc_final: 0.8494 (tp30) REVERT: B 168 GLU cc_start: 0.8501 (tt0) cc_final: 0.8008 (tt0) REVERT: B 170 GLU cc_start: 0.8898 (pp20) cc_final: 0.8675 (pp20) REVERT: B 220 ARG cc_start: 0.8459 (ttm110) cc_final: 0.7813 (mtt180) REVERT: B 236 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8774 (tppt) REVERT: B 302 ASP cc_start: 0.8054 (t0) cc_final: 0.7772 (t0) REVERT: B 320 ASP cc_start: 0.8875 (t0) cc_final: 0.8621 (t0) REVERT: C 45 MET cc_start: 0.7935 (mpm) cc_final: 0.7469 (mpp) REVERT: C 75 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8475 (mm) REVERT: C 77 LYS cc_start: 0.9172 (mmmm) cc_final: 0.8828 (mptt) REVERT: C 79 GLN cc_start: 0.8970 (pm20) cc_final: 0.8229 (pm20) REVERT: C 99 MET cc_start: 0.8544 (pmm) cc_final: 0.8292 (pmm) REVERT: C 108 MET cc_start: 0.8685 (mmm) cc_final: 0.8346 (mmt) REVERT: C 123 ASN cc_start: 0.9264 (p0) cc_final: 0.8989 (p0) REVERT: C 167 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8488 (tp30) REVERT: C 170 GLU cc_start: 0.8719 (pp20) cc_final: 0.8450 (pp20) REVERT: C 172 ARG cc_start: 0.9234 (ttp80) cc_final: 0.8393 (ptt90) REVERT: C 174 MET cc_start: 0.6838 (mmp) cc_final: 0.6142 (tpt) REVERT: C 237 ASP cc_start: 0.7778 (p0) cc_final: 0.7308 (p0) REVERT: C 244 ASP cc_start: 0.8468 (t70) cc_final: 0.7683 (t0) REVERT: C 285 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8083 (tm-30) REVERT: C 346 ASP cc_start: 0.7671 (t0) cc_final: 0.7368 (t0) REVERT: J 1 MET cc_start: 0.8109 (ttp) cc_final: 0.7753 (tmm) REVERT: J 10 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7296 (mmm) REVERT: J 23 ARG cc_start: 0.8188 (mpp-170) cc_final: 0.7689 (mpt180) REVERT: J 29 ASN cc_start: 0.7899 (t0) cc_final: 0.7644 (t0) REVERT: J 36 LYS cc_start: 0.8988 (tmmm) cc_final: 0.8575 (pttt) REVERT: I 10 MET cc_start: 0.8588 (mpp) cc_final: 0.8229 (mpp) REVERT: I 41 TYR cc_start: 0.7735 (t80) cc_final: 0.7287 (t80) REVERT: E 17 ASP cc_start: 0.8852 (m-30) cc_final: 0.8567 (m-30) REVERT: E 36 LYS cc_start: 0.8148 (pttm) cc_final: 0.7939 (pttm) REVERT: M 99 MET cc_start: 0.7553 (mmm) cc_final: 0.7039 (tpt) REVERT: M 129 GLN cc_start: 0.8193 (tp40) cc_final: 0.7552 (tp-100) REVERT: M 159 LYS cc_start: 0.9569 (ttmp) cc_final: 0.9257 (tppt) REVERT: M 289 GLN cc_start: 0.8789 (mp10) cc_final: 0.8486 (mp-120) REVERT: M 291 GLN cc_start: 0.9296 (tp-100) cc_final: 0.8728 (tp-100) REVERT: M 295 ASP cc_start: 0.9151 (p0) cc_final: 0.8744 (p0) REVERT: M 356 THR cc_start: 0.9322 (p) cc_final: 0.9011 (t) REVERT: M 359 MET cc_start: 0.7897 (tmm) cc_final: 0.7683 (tmm) REVERT: M 375 TRP cc_start: 0.6469 (m-10) cc_final: 0.6131 (m-10) REVERT: M 378 TYR cc_start: 0.9394 (p90) cc_final: 0.9036 (p90) REVERT: N 28 ASP cc_start: 0.8675 (p0) cc_final: 0.8450 (p0) REVERT: N 45 MET cc_start: 0.8508 (pmm) cc_final: 0.8069 (mpp) REVERT: N 51 ASN cc_start: 0.9268 (m110) cc_final: 0.8933 (t0) REVERT: N 92 MET cc_start: 0.9276 (mmm) cc_final: 0.8901 (mmm) REVERT: N 94 THR cc_start: 0.9211 (p) cc_final: 0.8721 (p) REVERT: N 115 ARG cc_start: 0.8649 (mtp85) cc_final: 0.8222 (mtm180) REVERT: N 126 VAL cc_start: 0.9523 (p) cc_final: 0.9267 (p) REVERT: N 128 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8904 (mmmt) REVERT: N 129 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8034 (mm-40) REVERT: N 139 ARG cc_start: 0.8411 (mmt90) cc_final: 0.7967 (mtp-110) REVERT: N 156 TYR cc_start: 0.9199 (t80) cc_final: 0.8791 (t80) REVERT: N 168 GLU cc_start: 0.9376 (pp20) cc_final: 0.8933 (pp20) REVERT: N 170 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8587 (tm-30) REVERT: N 171 MET cc_start: 0.9089 (ppp) cc_final: 0.8765 (ppp) REVERT: N 202 PHE cc_start: 0.9104 (t80) cc_final: 0.8867 (t80) REVERT: N 203 GLU cc_start: 0.8926 (pp20) cc_final: 0.8609 (tm-30) REVERT: N 217 GLU cc_start: 0.7864 (tp30) cc_final: 0.7539 (tp30) REVERT: N 220 ARG cc_start: 0.8849 (mtt180) cc_final: 0.8632 (ttp-170) REVERT: N 234 LYS cc_start: 0.9128 (mtpp) cc_final: 0.8731 (mmmt) REVERT: N 237 ASP cc_start: 0.8508 (p0) cc_final: 0.7674 (p0) REVERT: N 284 LYS cc_start: 0.9297 (mtmt) cc_final: 0.8953 (mtmm) REVERT: N 298 ARG cc_start: 0.9213 (mmt-90) cc_final: 0.8925 (mmp80) REVERT: N 302 ASP cc_start: 0.8575 (t0) cc_final: 0.8006 (t0) REVERT: N 346 ASP cc_start: 0.8614 (p0) cc_final: 0.8012 (p0) REVERT: N 377 HIS cc_start: 0.9111 (m90) cc_final: 0.8861 (m-70) REVERT: O 39 TRP cc_start: 0.9360 (t-100) cc_final: 0.8994 (t-100) REVERT: O 40 ASP cc_start: 0.9191 (t0) cc_final: 0.8959 (t70) REVERT: O 79 GLN cc_start: 0.8671 (mm110) cc_final: 0.8237 (mm110) REVERT: O 97 ILE cc_start: 0.9550 (pp) cc_final: 0.9189 (mp) REVERT: O 108 MET cc_start: 0.8095 (ptm) cc_final: 0.7798 (mtt) REVERT: O 153 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8504 (mm) REVERT: O 236 LYS cc_start: 0.9204 (pttp) cc_final: 0.8954 (ptpt) REVERT: O 370 ASP cc_start: 0.8398 (t70) cc_final: 0.8144 (t0) REVERT: Q 33 ASP cc_start: 0.8355 (t70) cc_final: 0.7897 (t70) REVERT: Q 39 ASP cc_start: 0.8385 (t70) cc_final: 0.8048 (t70) REVERT: S 10 MET cc_start: 0.8466 (mpt) cc_final: 0.8039 (mmt) REVERT: S 14 SER cc_start: 0.9618 (m) cc_final: 0.9325 (p) REVERT: S 49 SER cc_start: 0.9086 (t) cc_final: 0.8855 (p) outliers start: 108 outliers final: 46 residues processed: 667 average time/residue: 0.3937 time to fit residues: 386.5818 Evaluate side-chains 588 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 538 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain I residue 6 ASN Chi-restraints excluded: chain I residue 36 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 140 PHE Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 323 LYS Chi-restraints excluded: chain N residue 325 LYS Chi-restraints excluded: chain N residue 337 LYS Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 116 MET Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 153 LEU Chi-restraints excluded: chain O residue 287 LYS Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 81 optimal weight: 0.0050 chunk 209 optimal weight: 0.1980 chunk 247 optimal weight: 0.9980 chunk 258 optimal weight: 40.0000 chunk 156 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 chunk 64 optimal weight: 0.3980 chunk 249 optimal weight: 0.5980 chunk 70 optimal weight: 0.0060 chunk 234 optimal weight: 7.9990 overall best weight: 0.2410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 207 ASN A 290 ASN B 365 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN C 219 HIS I 46 HIS D 46 HIS E 5 ASN M 135 ASN N 129 GLN ** N 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.090547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.076520 restraints weight = 69628.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.078860 restraints weight = 37222.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080425 restraints weight = 23863.578| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22334 Z= 0.148 Angle : 0.829 12.133 30163 Z= 0.416 Chirality : 0.048 0.252 3370 Planarity : 0.004 0.046 3876 Dihedral : 6.984 43.376 2975 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 3.96 % Allowed : 18.98 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.31 (0.15), residues: 2555 helix: -1.31 (0.21), residues: 515 sheet: -2.35 (0.22), residues: 441 loop : -2.58 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 74 HIS 0.007 0.001 HIS I 46 PHE 0.019 0.001 PHE A 131 TYR 0.020 0.002 TYR C 319 ARG 0.009 0.001 ARG S 23 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 627) hydrogen bonds : angle 5.99359 ( 1665) covalent geometry : bond 0.00308 (22334) covalent geometry : angle 0.82883 (30163) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 632 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9163 (ptm160) cc_final: 0.8792 (ptm160) REVERT: A 84 GLN cc_start: 0.8392 (pt0) cc_final: 0.7329 (mp10) REVERT: A 127 LYS cc_start: 0.9529 (mptm) cc_final: 0.9134 (mmmm) REVERT: A 168 GLU cc_start: 0.9189 (tt0) cc_final: 0.8953 (tt0) REVERT: A 194 LYS cc_start: 0.9338 (tttp) cc_final: 0.8960 (tptt) REVERT: A 275 ASP cc_start: 0.8665 (t70) cc_final: 0.8406 (t0) REVERT: A 361 LYS cc_start: 0.9423 (mmmt) cc_final: 0.9190 (mmmt) REVERT: A 375 TRP cc_start: 0.8738 (m-90) cc_final: 0.8439 (m-10) REVERT: B 39 TRP cc_start: 0.9524 (t-100) cc_final: 0.9195 (t-100) REVERT: B 79 GLN cc_start: 0.8279 (pp30) cc_final: 0.7966 (pp30) REVERT: B 86 SER cc_start: 0.9220 (p) cc_final: 0.8814 (m) REVERT: B 99 MET cc_start: 0.8142 (ppp) cc_final: 0.7474 (tmm) REVERT: B 127 LYS cc_start: 0.9192 (mtpp) cc_final: 0.8702 (mmtp) REVERT: B 139 ARG cc_start: 0.8649 (mmt90) cc_final: 0.8199 (mtp-110) REVERT: B 170 GLU cc_start: 0.8865 (pp20) cc_final: 0.8593 (pp20) REVERT: B 220 ARG cc_start: 0.8389 (ttm110) cc_final: 0.7861 (mtt180) REVERT: B 236 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8675 (tppt) REVERT: B 302 ASP cc_start: 0.8039 (t0) cc_final: 0.7778 (t0) REVERT: B 375 TRP cc_start: 0.8924 (m-90) cc_final: 0.8497 (m-10) REVERT: C 45 MET cc_start: 0.7871 (mpm) cc_final: 0.7491 (mpp) REVERT: C 77 LYS cc_start: 0.9325 (mmmm) cc_final: 0.8838 (mmmm) REVERT: C 79 GLN cc_start: 0.8856 (pm20) cc_final: 0.8110 (pm20) REVERT: C 108 MET cc_start: 0.8659 (mmm) cc_final: 0.8225 (mmt) REVERT: C 123 ASN cc_start: 0.9263 (p0) cc_final: 0.8990 (p0) REVERT: C 167 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8675 (tp30) REVERT: C 172 ARG cc_start: 0.9250 (ttp80) cc_final: 0.8445 (ptt90) REVERT: C 174 MET cc_start: 0.6645 (mmp) cc_final: 0.5845 (tpt) REVERT: C 237 ASP cc_start: 0.7530 (p0) cc_final: 0.6998 (p0) REVERT: C 285 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 346 ASP cc_start: 0.7471 (t0) cc_final: 0.6888 (t0) REVERT: C 354 ARG cc_start: 0.8779 (ptp-170) cc_final: 0.8530 (ptp-170) REVERT: J 1 MET cc_start: 0.8083 (ttp) cc_final: 0.7806 (tmm) REVERT: J 10 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6842 (mmm) REVERT: J 21 ASN cc_start: 0.8929 (t0) cc_final: 0.8563 (t0) REVERT: I 10 MET cc_start: 0.8395 (mpp) cc_final: 0.7702 (mpp) REVERT: I 39 ASP cc_start: 0.8920 (p0) cc_final: 0.8705 (p0) REVERT: D 45 ILE cc_start: 0.6586 (tp) cc_final: 0.6361 (mp) REVERT: E 17 ASP cc_start: 0.8851 (m-30) cc_final: 0.8557 (m-30) REVERT: E 29 ASN cc_start: 0.8278 (m110) cc_final: 0.8076 (m-40) REVERT: E 30 MET cc_start: 0.8286 (tpp) cc_final: 0.7971 (tpp) REVERT: E 36 LYS cc_start: 0.7987 (pttm) cc_final: 0.7780 (pttm) REVERT: M 129 GLN cc_start: 0.7999 (tp40) cc_final: 0.7668 (tp-100) REVERT: M 159 LYS cc_start: 0.9528 (ttmp) cc_final: 0.9312 (tppt) REVERT: M 177 ASP cc_start: 0.8933 (p0) cc_final: 0.8702 (p0) REVERT: M 289 GLN cc_start: 0.8792 (mp10) cc_final: 0.8433 (mp-120) REVERT: M 291 GLN cc_start: 0.9278 (tp-100) cc_final: 0.8700 (tp-100) REVERT: M 295 ASP cc_start: 0.9099 (p0) cc_final: 0.8690 (p0) REVERT: M 378 TYR cc_start: 0.9381 (p90) cc_final: 0.9142 (p90) REVERT: N 28 ASP cc_start: 0.8690 (p0) cc_final: 0.8460 (p0) REVERT: N 45 MET cc_start: 0.8378 (pmm) cc_final: 0.7952 (mpp) REVERT: N 51 ASN cc_start: 0.9193 (m110) cc_final: 0.8735 (t0) REVERT: N 88 GLU cc_start: 0.7221 (pm20) cc_final: 0.6961 (pm20) REVERT: N 92 MET cc_start: 0.9207 (mmm) cc_final: 0.8710 (mmm) REVERT: N 94 THR cc_start: 0.9085 (p) cc_final: 0.8706 (p) REVERT: N 115 ARG cc_start: 0.8649 (mtp85) cc_final: 0.8200 (mtm180) REVERT: N 139 ARG cc_start: 0.8440 (mmt90) cc_final: 0.8016 (mtp-110) REVERT: N 156 TYR cc_start: 0.9099 (t80) cc_final: 0.8820 (t80) REVERT: N 168 GLU cc_start: 0.9328 (pp20) cc_final: 0.9118 (pt0) REVERT: N 170 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8407 (tm-30) REVERT: N 171 MET cc_start: 0.9160 (ppp) cc_final: 0.8809 (ppp) REVERT: N 203 GLU cc_start: 0.8889 (pp20) cc_final: 0.8616 (tm-30) REVERT: N 217 GLU cc_start: 0.7682 (tp30) cc_final: 0.7390 (tp30) REVERT: N 220 ARG cc_start: 0.8785 (mtt180) cc_final: 0.8531 (ttm170) REVERT: N 234 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8433 (mmmt) REVERT: N 237 ASP cc_start: 0.8311 (p0) cc_final: 0.7472 (p0) REVERT: N 252 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8761 (p0) REVERT: N 284 LYS cc_start: 0.9243 (mtmt) cc_final: 0.8899 (mtmm) REVERT: N 298 ARG cc_start: 0.9230 (mmt-90) cc_final: 0.8911 (mmp80) REVERT: N 346 ASP cc_start: 0.8603 (p0) cc_final: 0.7962 (p0) REVERT: N 382 LYS cc_start: 0.8857 (mttp) cc_final: 0.8261 (mttm) REVERT: O 39 TRP cc_start: 0.9346 (t-100) cc_final: 0.9046 (t-100) REVERT: O 40 ASP cc_start: 0.9171 (t0) cc_final: 0.8913 (t70) REVERT: O 79 GLN cc_start: 0.8596 (mm110) cc_final: 0.8306 (mm110) REVERT: O 92 MET cc_start: 0.8922 (mpp) cc_final: 0.8607 (mpp) REVERT: O 110 LYS cc_start: 0.9341 (mmtm) cc_final: 0.8952 (mmtm) REVERT: O 203 GLU cc_start: 0.8733 (pp20) cc_final: 0.8445 (pp20) REVERT: O 236 LYS cc_start: 0.9175 (pttp) cc_final: 0.8882 (ptpt) REVERT: Q 23 ARG cc_start: 0.8357 (pmm150) cc_final: 0.7694 (pmm150) REVERT: Q 33 ASP cc_start: 0.8162 (t70) cc_final: 0.7722 (t70) REVERT: S 10 MET cc_start: 0.8089 (mpt) cc_final: 0.7623 (mmp) REVERT: S 14 SER cc_start: 0.9563 (m) cc_final: 0.9355 (p) REVERT: S 27 ASN cc_start: 0.8596 (t0) cc_final: 0.8348 (p0) REVERT: S 49 SER cc_start: 0.8927 (t) cc_final: 0.8705 (p) outliers start: 92 outliers final: 38 residues processed: 680 average time/residue: 0.3688 time to fit residues: 374.5400 Evaluate side-chains 595 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 555 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 140 PHE Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 211 ASN Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 323 LYS Chi-restraints excluded: chain N residue 337 LYS Chi-restraints excluded: chain N residue 350 ILE Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 267 optimal weight: 40.0000 chunk 211 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 GLN N 219 HIS N 228 GLN O 23 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.087926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074098 restraints weight = 72527.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076348 restraints weight = 38963.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077874 restraints weight = 25184.520| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22334 Z= 0.181 Angle : 0.812 11.157 30163 Z= 0.410 Chirality : 0.048 0.276 3370 Planarity : 0.004 0.038 3876 Dihedral : 6.688 40.272 2975 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 4.82 % Allowed : 20.09 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.08 (0.15), residues: 2555 helix: -1.04 (0.22), residues: 524 sheet: -2.18 (0.22), residues: 445 loop : -2.47 (0.14), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 74 HIS 0.013 0.001 HIS N 377 PHE 0.018 0.001 PHE I 53 TYR 0.033 0.002 TYR O 178 ARG 0.005 0.001 ARG S 23 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 627) hydrogen bonds : angle 5.85075 ( 1665) covalent geometry : bond 0.00394 (22334) covalent geometry : angle 0.81174 (30163) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 571 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8523 (pt0) cc_final: 0.7466 (mp10) REVERT: A 127 LYS cc_start: 0.9522 (mptm) cc_final: 0.9084 (mmmm) REVERT: A 160 ILE cc_start: 0.9384 (pp) cc_final: 0.9154 (mt) REVERT: A 194 LYS cc_start: 0.9347 (tttp) cc_final: 0.8969 (tptt) REVERT: A 275 ASP cc_start: 0.8726 (t70) cc_final: 0.8425 (t0) REVERT: A 361 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9225 (mmmt) REVERT: A 375 TRP cc_start: 0.8815 (m-90) cc_final: 0.8445 (m-10) REVERT: B 39 TRP cc_start: 0.9548 (t-100) cc_final: 0.9299 (t-100) REVERT: B 92 MET cc_start: 0.8897 (mmm) cc_final: 0.8585 (mmm) REVERT: B 99 MET cc_start: 0.8224 (ppp) cc_final: 0.7559 (tmm) REVERT: B 139 ARG cc_start: 0.8592 (mmt90) cc_final: 0.8172 (mtp-110) REVERT: B 167 GLU cc_start: 0.8766 (tp30) cc_final: 0.8315 (tp30) REVERT: B 170 GLU cc_start: 0.8875 (pp20) cc_final: 0.8617 (pp20) REVERT: B 220 ARG cc_start: 0.8421 (ttm110) cc_final: 0.7833 (mtt180) REVERT: B 236 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8819 (tppt) REVERT: B 238 ILE cc_start: 0.9392 (pp) cc_final: 0.9029 (mp) REVERT: B 274 ASP cc_start: 0.8758 (m-30) cc_final: 0.8261 (p0) REVERT: B 302 ASP cc_start: 0.8086 (t0) cc_final: 0.7851 (t0) REVERT: B 375 TRP cc_start: 0.8916 (m-90) cc_final: 0.8408 (m-10) REVERT: C 45 MET cc_start: 0.7887 (mpm) cc_final: 0.7505 (mpp) REVERT: C 77 LYS cc_start: 0.9378 (mmmm) cc_final: 0.8914 (mmmm) REVERT: C 79 GLN cc_start: 0.8971 (pm20) cc_final: 0.8220 (pm20) REVERT: C 108 MET cc_start: 0.8635 (mmm) cc_final: 0.8226 (mmt) REVERT: C 110 LYS cc_start: 0.9502 (mtmm) cc_final: 0.9270 (mtmm) REVERT: C 123 ASN cc_start: 0.9274 (p0) cc_final: 0.8983 (p0) REVERT: C 168 GLU cc_start: 0.9468 (pp20) cc_final: 0.9057 (pp20) REVERT: C 172 ARG cc_start: 0.9254 (ttp80) cc_final: 0.8503 (ptt90) REVERT: C 174 MET cc_start: 0.6865 (mmp) cc_final: 0.6177 (tpt) REVERT: C 254 LYS cc_start: 0.9540 (OUTLIER) cc_final: 0.9260 (mmtt) REVERT: C 285 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 369 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7420 (t80) REVERT: J 10 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7098 (mmm) REVERT: J 21 ASN cc_start: 0.8946 (t0) cc_final: 0.8594 (t0) REVERT: I 10 MET cc_start: 0.8425 (mpp) cc_final: 0.8067 (mpp) REVERT: D 46 HIS cc_start: 0.6900 (OUTLIER) cc_final: 0.6328 (t70) REVERT: E 36 LYS cc_start: 0.7996 (pttm) cc_final: 0.7746 (pttm) REVERT: M 92 MET cc_start: 0.7545 (mtm) cc_final: 0.7266 (mtp) REVERT: M 129 GLN cc_start: 0.8105 (tp40) cc_final: 0.7594 (tp-100) REVERT: M 159 LYS cc_start: 0.9544 (ttmp) cc_final: 0.9245 (tppt) REVERT: M 180 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9362 (mm) REVERT: M 291 GLN cc_start: 0.9261 (tp-100) cc_final: 0.8621 (tp-100) REVERT: M 295 ASP cc_start: 0.9047 (p0) cc_final: 0.8607 (p0) REVERT: M 378 TYR cc_start: 0.9376 (p90) cc_final: 0.9156 (p90) REVERT: N 28 ASP cc_start: 0.8682 (p0) cc_final: 0.8454 (p0) REVERT: N 45 MET cc_start: 0.8426 (pmm) cc_final: 0.8050 (mpp) REVERT: N 51 ASN cc_start: 0.9175 (m110) cc_final: 0.8720 (t0) REVERT: N 88 GLU cc_start: 0.7316 (pm20) cc_final: 0.7107 (pm20) REVERT: N 92 MET cc_start: 0.9238 (mmm) cc_final: 0.8883 (mmm) REVERT: N 94 THR cc_start: 0.9119 (p) cc_final: 0.8672 (p) REVERT: N 110 LYS cc_start: 0.9491 (tppt) cc_final: 0.9108 (mmtt) REVERT: N 115 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8437 (mtm180) REVERT: N 139 ARG cc_start: 0.8438 (mmt90) cc_final: 0.7921 (mtp-110) REVERT: N 156 TYR cc_start: 0.9109 (t80) cc_final: 0.8843 (t80) REVERT: N 168 GLU cc_start: 0.9355 (pp20) cc_final: 0.8909 (pp20) REVERT: N 170 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8525 (tm-30) REVERT: N 171 MET cc_start: 0.9163 (ppp) cc_final: 0.8769 (ppp) REVERT: N 203 GLU cc_start: 0.8852 (pp20) cc_final: 0.8618 (tm-30) REVERT: N 217 GLU cc_start: 0.7876 (tp30) cc_final: 0.7530 (tp30) REVERT: N 220 ARG cc_start: 0.8776 (mtt180) cc_final: 0.8440 (ttm170) REVERT: N 234 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8489 (mmmt) REVERT: N 237 ASP cc_start: 0.8400 (p0) cc_final: 0.7652 (p0) REVERT: N 284 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8820 (mtmm) REVERT: N 346 ASP cc_start: 0.8642 (p0) cc_final: 0.8110 (p0) REVERT: N 375 TRP cc_start: 0.9352 (m-90) cc_final: 0.8649 (m-90) REVERT: N 382 LYS cc_start: 0.8884 (mttp) cc_final: 0.8600 (mttm) REVERT: O 39 TRP cc_start: 0.9311 (t-100) cc_final: 0.9030 (t-100) REVERT: O 40 ASP cc_start: 0.9174 (t0) cc_final: 0.8932 (t0) REVERT: O 92 MET cc_start: 0.8917 (mpp) cc_final: 0.8699 (mpp) REVERT: O 203 GLU cc_start: 0.8740 (pp20) cc_final: 0.8463 (pp20) REVERT: O 207 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8230 (m-40) REVERT: O 236 LYS cc_start: 0.9212 (pttp) cc_final: 0.8932 (ptpt) REVERT: Q 21 ASN cc_start: 0.8369 (t0) cc_final: 0.8090 (t0) REVERT: Q 23 ARG cc_start: 0.8430 (pmm150) cc_final: 0.7802 (pmm150) REVERT: Q 33 ASP cc_start: 0.8366 (t70) cc_final: 0.7832 (t70) REVERT: S 10 MET cc_start: 0.7917 (mpt) cc_final: 0.7515 (mmp) REVERT: S 21 ASN cc_start: 0.8073 (p0) cc_final: 0.7807 (p0) REVERT: S 45 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6524 (mm) REVERT: S 49 SER cc_start: 0.8974 (t) cc_final: 0.8750 (p) outliers start: 112 outliers final: 64 residues processed: 635 average time/residue: 0.3588 time to fit residues: 341.9764 Evaluate side-chains 610 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 539 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 241 LEU Chi-restraints excluded: chain N residue 257 ASN Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 323 LYS Chi-restraints excluded: chain N residue 337 LYS Chi-restraints excluded: chain N residue 347 ILE Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 116 MET Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 207 ASN Chi-restraints excluded: chain O residue 287 LYS Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 45 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 157 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 79 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 HIS N 164 ASN N 187 ASN N 211 ASN N 219 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.085624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071991 restraints weight = 73080.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.074128 restraints weight = 39082.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075641 restraints weight = 25454.381| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22334 Z= 0.251 Angle : 0.847 12.235 30163 Z= 0.427 Chirality : 0.050 0.289 3370 Planarity : 0.004 0.035 3876 Dihedral : 6.619 39.238 2975 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 5.42 % Allowed : 20.78 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.93 (0.16), residues: 2555 helix: -0.86 (0.22), residues: 522 sheet: -2.01 (0.22), residues: 459 loop : -2.41 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 74 HIS 0.026 0.002 HIS D 46 PHE 0.016 0.001 PHE A 202 TYR 0.026 0.002 TYR O 178 ARG 0.005 0.001 ARG M 115 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 627) hydrogen bonds : angle 5.87589 ( 1665) covalent geometry : bond 0.00545 (22334) covalent geometry : angle 0.84677 (30163) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 550 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.9541 (mptm) cc_final: 0.9057 (mmmm) REVERT: A 194 LYS cc_start: 0.9380 (tttp) cc_final: 0.8969 (tptt) REVERT: A 234 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8613 (mmmt) REVERT: A 275 ASP cc_start: 0.8833 (t70) cc_final: 0.8539 (t0) REVERT: A 361 LYS cc_start: 0.9556 (mmmt) cc_final: 0.9241 (mmmt) REVERT: A 375 TRP cc_start: 0.8851 (m-90) cc_final: 0.8470 (m-10) REVERT: B 39 TRP cc_start: 0.9573 (t-100) cc_final: 0.9353 (t-100) REVERT: B 92 MET cc_start: 0.8966 (mmm) cc_final: 0.8650 (mmm) REVERT: B 99 MET cc_start: 0.8355 (ppp) cc_final: 0.7794 (tmm) REVERT: B 127 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8865 (mmmm) REVERT: B 139 ARG cc_start: 0.8788 (mmt90) cc_final: 0.8332 (mtp-110) REVERT: B 158 LYS cc_start: 0.9598 (tppt) cc_final: 0.9371 (tptp) REVERT: B 170 GLU cc_start: 0.8921 (pp20) cc_final: 0.8642 (pp20) REVERT: B 236 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8827 (tppt) REVERT: B 238 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9102 (mp) REVERT: B 274 ASP cc_start: 0.8835 (m-30) cc_final: 0.8272 (p0) REVERT: B 375 TRP cc_start: 0.8995 (m-90) cc_final: 0.8513 (m-10) REVERT: C 45 MET cc_start: 0.7893 (mpm) cc_final: 0.7435 (mpp) REVERT: C 77 LYS cc_start: 0.9459 (mmmm) cc_final: 0.9066 (mmmm) REVERT: C 79 GLN cc_start: 0.9072 (pm20) cc_final: 0.8369 (pm20) REVERT: C 98 ASN cc_start: 0.9082 (m-40) cc_final: 0.8861 (m-40) REVERT: C 108 MET cc_start: 0.8704 (mmm) cc_final: 0.8472 (mmt) REVERT: C 123 ASN cc_start: 0.9303 (p0) cc_final: 0.9011 (p0) REVERT: C 167 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8812 (tp30) REVERT: C 168 GLU cc_start: 0.9428 (pp20) cc_final: 0.9012 (pp20) REVERT: C 172 ARG cc_start: 0.9259 (ttp80) cc_final: 0.8465 (ptt90) REVERT: C 285 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8121 (tm-30) REVERT: C 354 ARG cc_start: 0.8911 (ptp-170) cc_final: 0.8497 (ptp-170) REVERT: C 369 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7587 (t80) REVERT: J 1 MET cc_start: 0.7409 (tmm) cc_final: 0.6785 (tmm) REVERT: J 10 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7463 (mmm) REVERT: J 23 ARG cc_start: 0.8252 (mpp-170) cc_final: 0.7888 (mpt180) REVERT: J 33 ASP cc_start: 0.7940 (p0) cc_final: 0.7215 (p0) REVERT: J 36 LYS cc_start: 0.8356 (pttt) cc_final: 0.8002 (pttt) REVERT: I 10 MET cc_start: 0.8370 (mpp) cc_final: 0.7982 (mpp) REVERT: I 39 ASP cc_start: 0.8888 (p0) cc_final: 0.8625 (p0) REVERT: E 50 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8299 (tmtt) REVERT: M 129 GLN cc_start: 0.8179 (tp40) cc_final: 0.7860 (tp-100) REVERT: M 234 LYS cc_start: 0.8744 (mmmt) cc_final: 0.8515 (mmmt) REVERT: M 289 GLN cc_start: 0.8782 (mp10) cc_final: 0.8527 (mp-120) REVERT: M 291 GLN cc_start: 0.9234 (tp-100) cc_final: 0.8679 (tp-100) REVERT: M 295 ASP cc_start: 0.9035 (p0) cc_final: 0.8590 (p0) REVERT: M 378 TYR cc_start: 0.9414 (p90) cc_final: 0.9194 (p90) REVERT: N 28 ASP cc_start: 0.8658 (p0) cc_final: 0.8417 (p0) REVERT: N 45 MET cc_start: 0.8595 (pmm) cc_final: 0.8170 (mpp) REVERT: N 51 ASN cc_start: 0.9138 (m110) cc_final: 0.8764 (t0) REVERT: N 88 GLU cc_start: 0.7384 (pm20) cc_final: 0.7179 (pm20) REVERT: N 92 MET cc_start: 0.9274 (mmm) cc_final: 0.8953 (mmm) REVERT: N 110 LYS cc_start: 0.9502 (tppt) cc_final: 0.9076 (mmtt) REVERT: N 115 ARG cc_start: 0.8644 (mtp85) cc_final: 0.8373 (mtm180) REVERT: N 139 ARG cc_start: 0.8363 (mmt90) cc_final: 0.7904 (mtp-110) REVERT: N 156 TYR cc_start: 0.9162 (t80) cc_final: 0.8877 (t80) REVERT: N 168 GLU cc_start: 0.9409 (pp20) cc_final: 0.8967 (pp20) REVERT: N 170 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8528 (tm-30) REVERT: N 171 MET cc_start: 0.9189 (ppp) cc_final: 0.8782 (ppp) REVERT: N 203 GLU cc_start: 0.8893 (pp20) cc_final: 0.8651 (tm-30) REVERT: N 217 GLU cc_start: 0.8020 (tp30) cc_final: 0.7727 (tp30) REVERT: N 220 ARG cc_start: 0.8822 (mtt180) cc_final: 0.8445 (ttp-170) REVERT: N 234 LYS cc_start: 0.8936 (mtpp) cc_final: 0.8550 (mmmt) REVERT: N 237 ASP cc_start: 0.8484 (p0) cc_final: 0.7767 (p0) REVERT: N 284 LYS cc_start: 0.9198 (mtmt) cc_final: 0.8892 (mtmm) REVERT: N 346 ASP cc_start: 0.8663 (p0) cc_final: 0.8138 (p0) REVERT: N 375 TRP cc_start: 0.9418 (m-90) cc_final: 0.8806 (m-90) REVERT: N 382 LYS cc_start: 0.8867 (mttp) cc_final: 0.8521 (mttm) REVERT: O 93 ASP cc_start: 0.8949 (m-30) cc_final: 0.8563 (p0) REVERT: O 207 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8715 (m-40) REVERT: O 236 LYS cc_start: 0.9242 (pttp) cc_final: 0.8966 (ptpt) REVERT: Q 16 GLU cc_start: 0.8690 (mp0) cc_final: 0.8430 (pm20) REVERT: Q 21 ASN cc_start: 0.8409 (t0) cc_final: 0.8188 (t0) REVERT: Q 23 ARG cc_start: 0.8463 (pmm150) cc_final: 0.7853 (pmm150) REVERT: Q 33 ASP cc_start: 0.8407 (t70) cc_final: 0.7871 (t70) REVERT: S 10 MET cc_start: 0.7930 (mpt) cc_final: 0.5979 (ptm) REVERT: S 21 ASN cc_start: 0.7955 (p0) cc_final: 0.7715 (p0) REVERT: S 27 ASN cc_start: 0.8565 (t0) cc_final: 0.8312 (p0) REVERT: S 49 SER cc_start: 0.9097 (t) cc_final: 0.8896 (p) outliers start: 126 outliers final: 71 residues processed: 620 average time/residue: 0.3688 time to fit residues: 342.0489 Evaluate side-chains 586 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 511 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 19 ARG Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 140 PHE Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 231 THR Chi-restraints excluded: chain N residue 241 LEU Chi-restraints excluded: chain N residue 257 ASN Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 323 LYS Chi-restraints excluded: chain N residue 337 LYS Chi-restraints excluded: chain N residue 347 ILE Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 116 MET Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 153 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 207 ASN Chi-restraints excluded: chain O residue 287 LYS Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 70.7333 > 50: distance: 12 - 16: 23.178 distance: 16 - 17: 16.835 distance: 17 - 18: 6.296 distance: 18 - 19: 12.233 distance: 18 - 20: 48.194 distance: 21 - 22: 57.242 distance: 21 - 24: 9.096 distance: 22 - 28: 42.187 distance: 24 - 25: 38.861 distance: 25 - 26: 9.964 distance: 26 - 27: 4.454 distance: 28 - 29: 33.974 distance: 29 - 30: 32.740 distance: 29 - 32: 26.641 distance: 30 - 31: 3.853 distance: 30 - 36: 10.196 distance: 32 - 33: 23.839 distance: 36 - 37: 18.555 distance: 37 - 38: 8.780 distance: 37 - 40: 6.979 distance: 38 - 45: 31.166 distance: 40 - 41: 8.375 distance: 41 - 42: 6.104 distance: 42 - 43: 15.582 distance: 43 - 44: 29.407 distance: 45 - 46: 21.925 distance: 45 - 51: 13.423 distance: 46 - 47: 28.092 distance: 46 - 49: 36.328 distance: 47 - 48: 32.805 distance: 47 - 52: 12.404 distance: 49 - 50: 21.325 distance: 50 - 51: 37.234 distance: 52 - 53: 39.283 distance: 52 - 58: 24.700 distance: 53 - 54: 24.186 distance: 53 - 56: 19.016 distance: 54 - 55: 20.201 distance: 54 - 59: 24.942 distance: 56 - 57: 46.194 distance: 57 - 58: 42.045 distance: 59 - 60: 16.224 distance: 59 - 133: 28.237 distance: 60 - 61: 54.198 distance: 60 - 63: 4.338 distance: 61 - 62: 41.062 distance: 62 - 130: 31.121 distance: 63 - 64: 30.414 distance: 64 - 65: 12.504 distance: 64 - 66: 34.885 distance: 65 - 67: 9.934 distance: 66 - 68: 6.962 distance: 67 - 69: 30.306 distance: 68 - 69: 21.574 distance: 71 - 72: 23.774 distance: 71 - 74: 41.142 distance: 72 - 73: 9.217 distance: 72 - 80: 47.743 distance: 75 - 76: 37.653 distance: 75 - 77: 53.958 distance: 76 - 78: 38.497 distance: 80 - 81: 32.411 distance: 80 - 120: 23.604 distance: 81 - 82: 18.358 distance: 81 - 84: 25.989 distance: 82 - 83: 15.976 distance: 82 - 88: 20.209 distance: 83 - 117: 32.238 distance: 85 - 86: 18.902 distance: 88 - 89: 10.562 distance: 88 - 94: 33.014 distance: 89 - 90: 28.293 distance: 89 - 92: 39.986 distance: 90 - 91: 29.113 distance: 90 - 95: 25.157 distance: 92 - 93: 41.732 distance: 93 - 94: 32.820