Starting phenix.real_space_refine on Sun Jun 22 10:56:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o9z_0664/06_2025/6o9z_0664_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o9z_0664/06_2025/6o9z_0664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o9z_0664/06_2025/6o9z_0664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o9z_0664/06_2025/6o9z_0664.map" model { file = "/net/cci-nas-00/data/ceres_data/6o9z_0664/06_2025/6o9z_0664_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o9z_0664/06_2025/6o9z_0664_neut.cif" } resolution = 3.03 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= -0.011 sd= 0.787 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 124 5.16 5 C 16584 2.51 5 N 4335 2.21 5 O 4743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25788 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3172 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 407} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 151 Chain: "B" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3172 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 407} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 151 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2415 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 20, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2425 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 20, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2683 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 65 Chain: "F" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2683 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 65 Chain: "G" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2080 Classifications: {'peptide': 290} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 108 Chain: "H" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2080 Classifications: {'peptide': 290} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 108 Chain: "I" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1609 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 185 Chain: "J" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1609 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 185 Chain: "L" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 930 Classifications: {'peptide': 176} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 148} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 546 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 313 Chain: "M" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 930 Classifications: {'peptide': 176} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 148} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 546 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 313 Time building chain proxies: 14.87, per 1000 atoms: 0.58 Number of scatterers: 25788 At special positions: 0 Unit cell: (186.594, 171.798, 120.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 2 15.00 O 4743 8.00 N 4335 7.00 C 16584 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: 6.39 Conformation dependent library (CDL) restraints added in 3.3 seconds 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6850 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 34 sheets defined 43.8% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 98 through 108 removed outlier: 4.189A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.704A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 278 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 98 through 108 removed outlier: 4.190A pdb=" N LYS B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.704A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 278 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.616A pdb=" N MET C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.796A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.779A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 208 removed outlier: 3.572A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 296 through 304 removed outlier: 4.440A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.771A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.670A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 126 through 145 removed outlier: 3.574A pdb=" N GLN D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 155 through 158 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 208 removed outlier: 3.738A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.513A pdb=" N GLU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 304 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'E' and resid 191 through 196 removed outlier: 3.869A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 196' Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 239 Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.809A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 Processing helix chain 'E' and resid 312 through 325 removed outlier: 3.673A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'E' and resid 368 through 379 removed outlier: 3.889A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 418 through 430 removed outlier: 4.462A pdb=" N GLN E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.727A pdb=" N LEU E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 518 removed outlier: 3.718A pdb=" N VAL E 518 " --> pdb=" O VAL E 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 3.869A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET F 196 " --> pdb=" O THR F 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 196' Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 239 Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.809A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 Processing helix chain 'F' and resid 312 through 325 removed outlier: 3.673A pdb=" N GLN F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 353 Processing helix chain 'F' and resid 368 through 379 removed outlier: 3.888A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 418 through 430 removed outlier: 4.462A pdb=" N GLN F 422 " --> pdb=" O VAL F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 459 through 463 removed outlier: 3.726A pdb=" N LEU F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 518 removed outlier: 3.717A pdb=" N VAL F 518 " --> pdb=" O VAL F 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 16 Processing helix chain 'G' and resid 21 through 36 removed outlier: 3.705A pdb=" N ALA G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 60 removed outlier: 3.517A pdb=" N ASP G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 77 removed outlier: 4.106A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 116 removed outlier: 4.011A pdb=" N ARG G 108 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 179 through 183 removed outlier: 3.831A pdb=" N VAL G 183 " --> pdb=" O ASP G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 222 Processing helix chain 'G' and resid 247 through 252 Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 292 through 305 Processing helix chain 'H' and resid 3 through 16 Processing helix chain 'H' and resid 21 through 36 removed outlier: 3.705A pdb=" N ALA H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 60 removed outlier: 3.518A pdb=" N ASP H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 77 removed outlier: 4.106A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 116 removed outlier: 4.011A pdb=" N ARG H 108 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 179 through 183 removed outlier: 3.831A pdb=" N VAL H 183 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 222 Processing helix chain 'H' and resid 247 through 252 Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 292 through 305 Processing helix chain 'I' and resid 36 through 46 removed outlier: 3.574A pdb=" N VAL I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 68 removed outlier: 4.015A pdb=" N GLU I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 93 removed outlier: 3.917A pdb=" N ILE I 93 " --> pdb=" O SER I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 97 removed outlier: 3.670A pdb=" N LEU I 97 " --> pdb=" O TYR I 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 94 through 97' Processing helix chain 'I' and resid 114 through 124 removed outlier: 3.655A pdb=" N VAL I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 removed outlier: 3.635A pdb=" N LEU I 187 " --> pdb=" O LYS I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 218 removed outlier: 3.674A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 236 Processing helix chain 'I' and resid 282 through 292 removed outlier: 3.909A pdb=" N ARG I 286 " --> pdb=" O TRP I 282 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 46 removed outlier: 3.574A pdb=" N VAL J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 68 removed outlier: 4.016A pdb=" N GLU J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 93 removed outlier: 3.917A pdb=" N ILE J 93 " --> pdb=" O SER J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 97 removed outlier: 3.669A pdb=" N LEU J 97 " --> pdb=" O TYR J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 94 through 97' Processing helix chain 'J' and resid 114 through 124 removed outlier: 3.654A pdb=" N VAL J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.634A pdb=" N LEU J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 218 removed outlier: 3.675A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 236 Processing helix chain 'J' and resid 282 through 292 removed outlier: 3.910A pdb=" N ARG J 286 " --> pdb=" O TRP J 282 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP J 290 " --> pdb=" O ARG J 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 52 Processing helix chain 'L' and resid 90 through 118 Processing helix chain 'L' and resid 122 through 142 removed outlier: 3.510A pdb=" N LEU L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 158 removed outlier: 3.650A pdb=" N TYR L 149 " --> pdb=" O GLY L 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER L 157 " --> pdb=" O LYS L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 163 Processing helix chain 'L' and resid 168 through 180 removed outlier: 3.614A pdb=" N ARG L 172 " --> pdb=" O ASN L 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 52 Processing helix chain 'M' and resid 90 through 118 Processing helix chain 'M' and resid 122 through 142 removed outlier: 3.510A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 158 removed outlier: 3.651A pdb=" N TYR M 149 " --> pdb=" O GLY M 145 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER M 157 " --> pdb=" O LYS M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 163 Processing helix chain 'M' and resid 168 through 180 removed outlier: 3.615A pdb=" N ARG M 172 " --> pdb=" O ASN M 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124 removed outlier: 7.515A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA A 45 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE A 94 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU A 47 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN A 44 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL A 151 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL A 46 " --> pdb=" O VAL A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 246 removed outlier: 4.684A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA A 204 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE A 215 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 202 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE I 157 " --> pdb=" O MET I 170 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET I 170 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY I 159 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.621A pdb=" N PHE A 224 " --> pdb=" O ILE I 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 337 removed outlier: 6.683A pdb=" N TYR A 343 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.382A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.864A pdb=" N VAL A 367 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS A 384 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 411 through 413 removed outlier: 6.057A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 458 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 450 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 122 through 124 removed outlier: 7.515A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA B 45 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE B 94 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU B 47 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN B 44 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL B 151 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL B 46 " --> pdb=" O VAL B 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB2, first strand: chain 'B' and resid 244 through 246 removed outlier: 4.683A pdb=" N ILE B 287 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA B 204 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE B 215 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 202 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE J 157 " --> pdb=" O MET J 170 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET J 170 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY J 159 " --> pdb=" O LEU J 168 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.596A pdb=" N PHE B 224 " --> pdb=" O ILE J 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.683A pdb=" N TYR B 343 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.381A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 367 through 368 removed outlier: 6.864A pdb=" N VAL B 367 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS B 384 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 411 through 413 removed outlier: 6.057A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 458 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 450 " --> pdb=" O GLU B 458 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.610A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE C 168 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL C 189 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N MET C 217 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 191 " --> pdb=" O MET C 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AC1, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.166A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL F 358 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU F 386 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL F 360 " --> pdb=" O LEU F 386 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.052A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL D 189 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N MET D 217 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL D 191 " --> pdb=" O MET D 217 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AC4, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.160A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL E 358 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU E 386 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL E 360 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL E 332 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU E 402 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU E 334 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY E 404 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR E 336 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AC6, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AC7, first strand: chain 'G' and resid 175 through 178 removed outlier: 8.545A pdb=" N THR G 176 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA G 123 " --> pdb=" O SER G 149 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR G 151 " --> pdb=" O ALA G 123 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE G 125 " --> pdb=" O TYR G 151 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR G 153 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR G 127 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N THR G 124 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE G 194 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU G 126 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AC9, first strand: chain 'H' and resid 175 through 178 removed outlier: 8.546A pdb=" N THR H 176 " --> pdb=" O PHE H 148 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA H 123 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR H 151 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE H 125 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR H 153 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR H 127 " --> pdb=" O THR H 153 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AD2, first strand: chain 'I' and resid 75 through 78 removed outlier: 8.531A pdb=" N ILE I 52 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA I 5 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL I 54 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL I 7 " --> pdb=" O VAL I 54 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 200 through 201 removed outlier: 6.429A pdb=" N LEU I 128 " --> pdb=" O TYR I 264 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE I 266 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET I 130 " --> pdb=" O PHE I 266 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 75 through 78 removed outlier: 8.530A pdb=" N ILE J 52 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA J 5 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL J 54 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL J 7 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN J 4 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU J 104 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL J 6 " --> pdb=" O LEU J 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 200 through 201 removed outlier: 6.430A pdb=" N LEU J 128 " --> pdb=" O TYR J 264 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE J 266 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET J 130 " --> pdb=" O PHE J 266 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 18 through 26 removed outlier: 6.912A pdb=" N TYR L 32 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE L 26 " --> pdb=" O GLY L 30 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLU L 42 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LEU L 84 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET L 44 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER L 85 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL L 72 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 18 through 26 removed outlier: 6.913A pdb=" N TYR M 32 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE M 26 " --> pdb=" O GLY M 30 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY M 30 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLU M 42 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LEU M 84 " --> pdb=" O GLU M 42 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET M 44 " --> pdb=" O LEU M 84 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER M 85 " --> pdb=" O VAL M 72 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL M 72 " --> pdb=" O SER M 85 " (cutoff:3.500A) 1171 hydrogen bonds defined for protein. 3315 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: 9.30 Time building geometry restraints manager: 7.45 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: 8528 1.34 - 1.46: 4992 1.46 - 1.58: 12495 1.58 - 1.70: 8 1.70 - 1.81: 190 Bond restraints: 26213 Sorted by residual: bond pdb=" CD2 TRP A 97 " pdb=" CE2 TRP A 97 " ideal model delta sigma weight residual 1.409 1.445 -0.036 1.70e-02 3.46e+03 4.37e+00 bond pdb=" CD2 TRP C 51 " pdb=" CE2 TRP C 51 " ideal model delta sigma weight residual 1.409 1.444 -0.035 1.70e-02 3.46e+03 4.32e+00 bond pdb=" CD2 TRP B 97 " pdb=" CE2 TRP B 97 " ideal model delta sigma weight residual 1.409 1.444 -0.035 1.70e-02 3.46e+03 4.21e+00 bond pdb=" CD2 TRP D 51 " pdb=" CE2 TRP D 51 " ideal model delta sigma weight residual 1.409 1.443 -0.034 1.70e-02 3.46e+03 4.01e+00 bond pdb=" CD2 TRP F 476 " pdb=" CE2 TRP F 476 " ideal model delta sigma weight residual 1.409 1.441 -0.032 1.70e-02 3.46e+03 3.52e+00 ... (remaining 26208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 34347 2.21 - 4.42: 1078 4.42 - 6.63: 140 6.63 - 8.84: 24 8.84 - 11.05: 10 Bond angle restraints: 35599 Sorted by residual: angle pdb=" N GLN G 156 " pdb=" CA GLN G 156 " pdb=" C GLN G 156 " ideal model delta sigma weight residual 109.81 119.94 -10.13 2.21e+00 2.05e-01 2.10e+01 angle pdb=" N GLN H 156 " pdb=" CA GLN H 156 " pdb=" C GLN H 156 " ideal model delta sigma weight residual 109.81 119.94 -10.13 2.21e+00 2.05e-01 2.10e+01 angle pdb=" N ALA G 295 " pdb=" CA ALA G 295 " pdb=" C ALA G 295 " ideal model delta sigma weight residual 113.23 107.63 5.60 1.24e+00 6.50e-01 2.04e+01 angle pdb=" N ALA H 295 " pdb=" CA ALA H 295 " pdb=" C ALA H 295 " ideal model delta sigma weight residual 113.23 107.65 5.58 1.24e+00 6.50e-01 2.03e+01 angle pdb=" N CYS H 57 " pdb=" CA CYS H 57 " pdb=" C CYS H 57 " ideal model delta sigma weight residual 113.41 108.22 5.19 1.22e+00 6.72e-01 1.81e+01 ... (remaining 35594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 14776 17.32 - 34.65: 831 34.65 - 51.97: 147 51.97 - 69.30: 38 69.30 - 86.62: 27 Dihedral angle restraints: 15819 sinusoidal: 5384 harmonic: 10435 Sorted by residual: dihedral pdb=" CA ASN D 242 " pdb=" C ASN D 242 " pdb=" N GLY D 243 " pdb=" CA GLY D 243 " ideal model delta harmonic sigma weight residual 180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA LYS G 209 " pdb=" C LYS G 209 " pdb=" N ILE G 210 " pdb=" CA ILE G 210 " ideal model delta harmonic sigma weight residual -180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA LYS H 209 " pdb=" C LYS H 209 " pdb=" N ILE H 210 " pdb=" CA ILE H 210 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 15816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3329 0.060 - 0.119: 938 0.119 - 0.179: 103 0.179 - 0.238: 15 0.238 - 0.298: 2 Chirality restraints: 4387 Sorted by residual: chirality pdb=" CB VAL G 236 " pdb=" CA VAL G 236 " pdb=" CG1 VAL G 236 " pdb=" CG2 VAL G 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB VAL H 236 " pdb=" CA VAL H 236 " pdb=" CG1 VAL H 236 " pdb=" CG2 VAL H 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA MET H 1 " pdb=" N MET H 1 " pdb=" C MET H 1 " pdb=" CB MET H 1 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4384 not shown) Planarity restraints: 4526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 294 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.69e+01 pdb=" C SER H 294 " 0.071 2.00e-02 2.50e+03 pdb=" O SER H 294 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA H 295 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 294 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C SER G 294 " 0.071 2.00e-02 2.50e+03 pdb=" O SER G 294 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA G 295 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 368 " 0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLU E 368 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU E 368 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY E 369 " 0.019 2.00e-02 2.50e+03 ... (remaining 4523 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3076 2.73 - 3.28: 25377 3.28 - 3.82: 42446 3.82 - 4.36: 49353 4.36 - 4.90: 86023 Nonbonded interactions: 206275 Sorted by model distance: nonbonded pdb=" OE1 GLU D 193 " pdb=" NE2 HIS D 201 " model vdw 2.192 3.120 nonbonded pdb=" OG1 THR F 440 " pdb=" OE2 GLU F 503 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR E 440 " pdb=" OE2 GLU E 503 " model vdw 2.236 3.040 nonbonded pdb=" NE2 GLN H 243 " pdb=" O TYR H 275 " model vdw 2.238 3.120 nonbonded pdb=" NE2 GLN G 243 " pdb=" O TYR G 275 " model vdw 2.239 3.120 ... (remaining 206270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 1.060 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 57.230 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.130 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 0.071 26213 Z= 0.357 Angle : 0.929 11.048 35599 Z= 0.522 Chirality : 0.054 0.298 4387 Planarity : 0.007 0.057 4526 Dihedral : 12.406 86.619 8969 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.48 % Allowed : 5.13 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.12), residues: 3555 helix: -1.78 (0.11), residues: 1387 sheet: -2.11 (0.22), residues: 471 loop : -2.10 (0.13), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP I 37 HIS 0.011 0.002 HIS B 105 PHE 0.036 0.003 PHE H 239 TYR 0.022 0.002 TYR D 335 ARG 0.003 0.000 ARG E 517 Details of bonding type rmsd hydrogen bonds : bond 0.16505 ( 1171) hydrogen bonds : angle 6.52699 ( 3315) covalent geometry : bond 0.00783 (26213) covalent geometry : angle 0.92890 (35599) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 763 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7510 (t0) cc_final: 0.7110 (t0) REVERT: A 276 LEU cc_start: 0.8888 (tp) cc_final: 0.8677 (tp) REVERT: A 312 ASP cc_start: 0.7983 (m-30) cc_final: 0.7702 (m-30) REVERT: B 50 ASP cc_start: 0.7656 (t0) cc_final: 0.7269 (t0) REVERT: C 20 GLU cc_start: 0.8684 (tt0) cc_final: 0.7676 (tm-30) REVERT: C 44 GLN cc_start: 0.8018 (tt0) cc_final: 0.7745 (tt0) REVERT: C 48 ASP cc_start: 0.8029 (m-30) cc_final: 0.7755 (m-30) REVERT: C 68 MET cc_start: 0.8423 (mtp) cc_final: 0.7707 (ttp) REVERT: C 96 LEU cc_start: 0.7568 (mt) cc_final: 0.7359 (tt) REVERT: C 163 GLU cc_start: 0.7479 (tt0) cc_final: 0.7176 (tt0) REVERT: C 209 LYS cc_start: 0.9138 (mttt) cc_final: 0.8911 (mtmt) REVERT: C 237 LYS cc_start: 0.8490 (tptt) cc_final: 0.8242 (tptp) REVERT: D 44 GLN cc_start: 0.8007 (tt0) cc_final: 0.7766 (tt0) REVERT: D 242 ASN cc_start: 0.8588 (m110) cc_final: 0.8235 (m-40) REVERT: E 236 VAL cc_start: 0.9101 (t) cc_final: 0.8847 (t) REVERT: E 362 ASP cc_start: 0.8445 (t0) cc_final: 0.8239 (t0) REVERT: E 439 GLU cc_start: 0.8692 (mp0) cc_final: 0.8115 (mp0) REVERT: E 462 ASP cc_start: 0.8437 (m-30) cc_final: 0.8205 (m-30) REVERT: F 236 VAL cc_start: 0.9100 (t) cc_final: 0.8850 (t) REVERT: F 362 ASP cc_start: 0.8436 (t0) cc_final: 0.8184 (t70) REVERT: F 367 LEU cc_start: 0.9186 (mt) cc_final: 0.8975 (mm) REVERT: F 439 GLU cc_start: 0.8701 (mp0) cc_final: 0.8125 (mp0) REVERT: F 462 ASP cc_start: 0.8433 (m-30) cc_final: 0.8190 (m-30) REVERT: G 17 ASP cc_start: 0.8305 (t0) cc_final: 0.8046 (t0) REVERT: G 75 PHE cc_start: 0.8835 (t80) cc_final: 0.8291 (t80) REVERT: G 187 MET cc_start: 0.8889 (tpp) cc_final: 0.8604 (tpt) REVERT: G 244 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8287 (tp40) REVERT: G 245 ASP cc_start: 0.8804 (t0) cc_final: 0.8455 (t0) REVERT: G 290 VAL cc_start: 0.9384 (t) cc_final: 0.9074 (t) REVERT: H 17 ASP cc_start: 0.8312 (t0) cc_final: 0.8079 (t0) REVERT: H 75 PHE cc_start: 0.8861 (t80) cc_final: 0.8281 (t80) REVERT: H 187 MET cc_start: 0.8886 (tpp) cc_final: 0.8471 (tpt) REVERT: H 244 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8274 (tp40) REVERT: H 245 ASP cc_start: 0.8854 (t0) cc_final: 0.8521 (t0) REVERT: H 290 VAL cc_start: 0.9357 (t) cc_final: 0.8953 (t) REVERT: I 125 ASP cc_start: 0.8826 (t70) cc_final: 0.8527 (t0) REVERT: I 161 ASP cc_start: 0.7032 (t70) cc_final: 0.6816 (p0) REVERT: J 125 ASP cc_start: 0.8774 (t70) cc_final: 0.8484 (t0) outliers start: 12 outliers final: 2 residues processed: 769 average time/residue: 0.3298 time to fit residues: 411.6467 Evaluate side-chains 554 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 552 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 76 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 323 optimal weight: 50.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS B 393 GLN C 188 HIS C 261 HIS D 132 ASN D 242 ASN D 261 HIS E 234 GLN E 245 ASN E 274 HIS E 281 ASN E 378 HIS E 422 GLN F 234 GLN F 245 ASN F 274 HIS F 281 ASN F 378 HIS ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS H 128 HIS I 115 HIS I 188 GLN J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.149171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118626 restraints weight = 47418.994| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.61 r_work: 0.3443 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26213 Z= 0.167 Angle : 0.613 9.282 35599 Z= 0.338 Chirality : 0.045 0.167 4387 Planarity : 0.004 0.055 4526 Dihedral : 4.630 32.087 3615 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.50 % Allowed : 14.51 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 3555 helix: 0.01 (0.13), residues: 1437 sheet: -1.74 (0.22), residues: 512 loop : -1.31 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 37 HIS 0.007 0.001 HIS F 378 PHE 0.021 0.001 PHE D 278 TYR 0.013 0.001 TYR B 78 ARG 0.004 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 1171) hydrogen bonds : angle 4.47171 ( 3315) covalent geometry : bond 0.00368 (26213) covalent geometry : angle 0.61299 (35599) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 648 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8383 (t0) cc_final: 0.8006 (t0) REVERT: A 160 ASN cc_start: 0.9007 (t0) cc_final: 0.8771 (t0) REVERT: A 276 LEU cc_start: 0.9029 (tp) cc_final: 0.8824 (tp) REVERT: A 295 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8396 (mt-10) REVERT: A 324 GLU cc_start: 0.9101 (pm20) cc_final: 0.8844 (pm20) REVERT: A 333 GLN cc_start: 0.8349 (mt0) cc_final: 0.8091 (mm-40) REVERT: B 50 ASP cc_start: 0.8474 (t0) cc_final: 0.8129 (t0) REVERT: B 104 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8373 (tp30) REVERT: B 160 ASN cc_start: 0.8976 (t0) cc_final: 0.8753 (t0) REVERT: B 324 GLU cc_start: 0.9135 (pm20) cc_final: 0.8844 (pm20) REVERT: C 44 GLN cc_start: 0.7843 (tt0) cc_final: 0.7507 (tt0) REVERT: C 48 ASP cc_start: 0.8177 (m-30) cc_final: 0.7852 (m-30) REVERT: C 96 LEU cc_start: 0.7624 (mt) cc_final: 0.7417 (tt) REVERT: D 16 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8548 (mm-30) REVERT: D 23 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8178 (mtpt) REVERT: D 164 VAL cc_start: 0.8910 (t) cc_final: 0.8655 (m) REVERT: D 217 MET cc_start: 0.8685 (ptt) cc_final: 0.8303 (ptt) REVERT: E 362 ASP cc_start: 0.8898 (t0) cc_final: 0.8656 (t70) REVERT: E 439 GLU cc_start: 0.9113 (mp0) cc_final: 0.8306 (mp0) REVERT: E 462 ASP cc_start: 0.8583 (m-30) cc_final: 0.8163 (m-30) REVERT: F 275 ASN cc_start: 0.8515 (t0) cc_final: 0.8314 (t0) REVERT: F 362 ASP cc_start: 0.8916 (t0) cc_final: 0.8667 (t70) REVERT: F 367 LEU cc_start: 0.9203 (mt) cc_final: 0.8933 (mm) REVERT: F 439 GLU cc_start: 0.9104 (mp0) cc_final: 0.8309 (mp0) REVERT: F 462 ASP cc_start: 0.8554 (m-30) cc_final: 0.8120 (m-30) REVERT: G 17 ASP cc_start: 0.8417 (t0) cc_final: 0.8113 (t0) REVERT: G 75 PHE cc_start: 0.9017 (t80) cc_final: 0.8368 (t80) REVERT: H 17 ASP cc_start: 0.8415 (t0) cc_final: 0.8116 (t0) REVERT: H 75 PHE cc_start: 0.8998 (t80) cc_final: 0.8285 (t80) REVERT: H 156 GLN cc_start: 0.8824 (tp40) cc_final: 0.8492 (tp40) REVERT: H 290 VAL cc_start: 0.9299 (t) cc_final: 0.9008 (t) REVERT: I 2 GLU cc_start: 0.4610 (tt0) cc_final: 0.4311 (tt0) REVERT: I 125 ASP cc_start: 0.9064 (t70) cc_final: 0.8839 (t0) REVERT: I 130 MET cc_start: 0.5944 (tmm) cc_final: 0.5718 (tmm) REVERT: I 161 ASP cc_start: 0.7203 (t70) cc_final: 0.6685 (p0) REVERT: I 165 LYS cc_start: 0.7488 (mtpt) cc_final: 0.7158 (mtpp) REVERT: I 183 LYS cc_start: 0.7150 (mtpt) cc_final: 0.6611 (mtmt) REVERT: J 2 GLU cc_start: 0.5314 (tt0) cc_final: 0.5054 (tt0) REVERT: J 125 ASP cc_start: 0.8979 (t70) cc_final: 0.8744 (t0) REVERT: J 130 MET cc_start: 0.6058 (tmm) cc_final: 0.5649 (tmm) REVERT: J 132 MET cc_start: 0.7279 (mtt) cc_final: 0.6816 (mtm) REVERT: J 161 ASP cc_start: 0.7464 (t70) cc_final: 0.6701 (p0) REVERT: J 199 LEU cc_start: 0.6195 (mt) cc_final: 0.5549 (mt) outliers start: 63 outliers final: 45 residues processed: 676 average time/residue: 0.3271 time to fit residues: 365.6472 Evaluate side-chains 592 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 547 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 196 MET Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 263 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 166 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 352 HIS ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 ASN E 265 GLN E 274 HIS E 430 HIS E 431 ASN F 265 GLN F 274 HIS F 422 GLN F 430 HIS H 213 ASN I 115 HIS J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.146440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115961 restraints weight = 47343.452| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.64 r_work: 0.3413 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26213 Z= 0.173 Angle : 0.587 8.737 35599 Z= 0.323 Chirality : 0.044 0.181 4387 Planarity : 0.004 0.053 4526 Dihedral : 4.437 30.867 3615 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.06 % Allowed : 16.98 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3555 helix: 0.89 (0.14), residues: 1421 sheet: -1.44 (0.22), residues: 520 loop : -1.05 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 97 HIS 0.007 0.001 HIS I 115 PHE 0.016 0.001 PHE D 177 TYR 0.010 0.001 TYR D 335 ARG 0.001 0.000 ARG G 108 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 1171) hydrogen bonds : angle 4.18898 ( 3315) covalent geometry : bond 0.00386 (26213) covalent geometry : angle 0.58745 (35599) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 579 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8361 (t0) cc_final: 0.7729 (t0) REVERT: A 160 ASN cc_start: 0.9036 (t0) cc_final: 0.8805 (t0) REVERT: A 217 LYS cc_start: 0.8995 (mttp) cc_final: 0.8592 (mmtm) REVERT: A 270 ASP cc_start: 0.8568 (m-30) cc_final: 0.7993 (m-30) REVERT: A 276 LEU cc_start: 0.9091 (tp) cc_final: 0.8834 (tp) REVERT: A 295 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8400 (mt-10) REVERT: A 324 GLU cc_start: 0.9122 (pm20) cc_final: 0.8715 (pm20) REVERT: A 423 VAL cc_start: 0.8719 (t) cc_final: 0.8428 (t) REVERT: B 50 ASP cc_start: 0.8424 (t0) cc_final: 0.7794 (t0) REVERT: B 160 ASN cc_start: 0.8999 (t0) cc_final: 0.8792 (t0) REVERT: B 167 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7814 (mm-30) REVERT: B 295 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8391 (mt-10) REVERT: B 324 GLU cc_start: 0.9174 (pm20) cc_final: 0.8790 (pm20) REVERT: C 20 GLU cc_start: 0.8913 (tt0) cc_final: 0.8117 (tp30) REVERT: C 32 GLU cc_start: 0.8984 (tt0) cc_final: 0.7970 (tm-30) REVERT: C 44 GLN cc_start: 0.7819 (tt0) cc_final: 0.7512 (tt0) REVERT: C 48 ASP cc_start: 0.8165 (m-30) cc_final: 0.7928 (m-30) REVERT: C 64 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8261 (tm-30) REVERT: C 163 GLU cc_start: 0.8533 (tt0) cc_final: 0.8325 (tt0) REVERT: C 293 GLU cc_start: 0.9085 (mp0) cc_final: 0.8832 (mp0) REVERT: D 217 MET cc_start: 0.8769 (ptt) cc_final: 0.8454 (ptt) REVERT: D 303 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8679 (mp) REVERT: E 310 GLU cc_start: 0.8363 (pt0) cc_final: 0.7958 (mt-10) REVERT: E 362 ASP cc_start: 0.8895 (t0) cc_final: 0.8654 (t70) REVERT: E 439 GLU cc_start: 0.9087 (mp0) cc_final: 0.8291 (mp0) REVERT: E 462 ASP cc_start: 0.8592 (m-30) cc_final: 0.8080 (m-30) REVERT: F 310 GLU cc_start: 0.8362 (pt0) cc_final: 0.7957 (mt-10) REVERT: F 367 LEU cc_start: 0.9244 (mt) cc_final: 0.8945 (mm) REVERT: F 439 GLU cc_start: 0.9064 (mp0) cc_final: 0.8119 (mp0) REVERT: F 461 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: G 17 ASP cc_start: 0.8459 (t0) cc_final: 0.8171 (t0) REVERT: G 75 PHE cc_start: 0.9036 (t80) cc_final: 0.8359 (t80) REVERT: G 164 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8238 (ttt) REVERT: G 231 GLU cc_start: 0.8765 (mp0) cc_final: 0.8438 (mp0) REVERT: H 17 ASP cc_start: 0.8460 (t0) cc_final: 0.8180 (t0) REVERT: H 75 PHE cc_start: 0.9019 (t80) cc_final: 0.8273 (t80) REVERT: H 164 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8086 (ttt) REVERT: H 290 VAL cc_start: 0.9325 (t) cc_final: 0.9057 (t) REVERT: I 99 THR cc_start: 0.6535 (OUTLIER) cc_final: 0.6257 (t) REVERT: I 130 MET cc_start: 0.6143 (tmm) cc_final: 0.5853 (tmm) REVERT: I 165 LYS cc_start: 0.7418 (mtpt) cc_final: 0.7206 (mtpt) REVERT: J 2 GLU cc_start: 0.5378 (tt0) cc_final: 0.4940 (tt0) REVERT: J 132 MET cc_start: 0.7290 (mtt) cc_final: 0.7057 (mtt) REVERT: J 161 ASP cc_start: 0.7557 (t70) cc_final: 0.6767 (p0) outliers start: 102 outliers final: 75 residues processed: 631 average time/residue: 0.3781 time to fit residues: 400.2363 Evaluate side-chains 614 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 534 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 196 MET Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 461 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 206 CYS Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 114 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 296 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS B 352 HIS C 154 GLN C 331 ASN D 132 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN F 234 GLN F 431 ASN I 115 HIS J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.144487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.114101 restraints weight = 48113.127| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.67 r_work: 0.3384 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26213 Z= 0.187 Angle : 0.596 9.259 35599 Z= 0.327 Chirality : 0.045 0.176 4387 Planarity : 0.004 0.051 4526 Dihedral : 4.462 31.735 3615 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.49 % Allowed : 18.21 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3555 helix: 1.21 (0.14), residues: 1423 sheet: -1.30 (0.22), residues: 530 loop : -0.93 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 37 HIS 0.007 0.001 HIS I 115 PHE 0.019 0.001 PHE D 177 TYR 0.012 0.001 TYR A 128 ARG 0.001 0.000 ARG G 74 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 1171) hydrogen bonds : angle 4.13224 ( 3315) covalent geometry : bond 0.00423 (26213) covalent geometry : angle 0.59649 (35599) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 548 time to evaluate : 4.285 Fit side-chains REVERT: A 50 ASP cc_start: 0.8277 (t0) cc_final: 0.7602 (t0) REVERT: A 107 LEU cc_start: 0.8542 (tp) cc_final: 0.8295 (mp) REVERT: A 160 ASN cc_start: 0.9061 (t0) cc_final: 0.8830 (t0) REVERT: A 217 LYS cc_start: 0.8946 (mttp) cc_final: 0.8499 (mmtm) REVERT: A 270 ASP cc_start: 0.8556 (m-30) cc_final: 0.7964 (m-30) REVERT: A 276 LEU cc_start: 0.9113 (tp) cc_final: 0.8826 (tp) REVERT: A 295 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8378 (mt-10) REVERT: A 324 GLU cc_start: 0.9129 (pm20) cc_final: 0.8611 (pm20) REVERT: A 418 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: A 423 VAL cc_start: 0.8794 (t) cc_final: 0.8547 (t) REVERT: B 50 ASP cc_start: 0.8336 (t0) cc_final: 0.7684 (t0) REVERT: B 160 ASN cc_start: 0.9017 (t0) cc_final: 0.8810 (t0) REVERT: B 167 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7847 (mm-30) REVERT: B 295 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8409 (mt-10) REVERT: B 324 GLU cc_start: 0.9149 (pm20) cc_final: 0.8625 (pm20) REVERT: C 20 GLU cc_start: 0.8928 (tt0) cc_final: 0.8157 (tp30) REVERT: C 32 GLU cc_start: 0.9047 (tt0) cc_final: 0.8046 (tm-30) REVERT: C 44 GLN cc_start: 0.7858 (tt0) cc_final: 0.7518 (tt0) REVERT: C 48 ASP cc_start: 0.8110 (m-30) cc_final: 0.7892 (m-30) REVERT: C 303 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8718 (mp) REVERT: C 305 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8635 (mmtp) REVERT: D 86 LEU cc_start: 0.8783 (tt) cc_final: 0.8546 (tt) REVERT: D 163 GLU cc_start: 0.8312 (tt0) cc_final: 0.8099 (tt0) REVERT: D 303 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8710 (mp) REVERT: D 305 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8697 (mmtp) REVERT: E 207 MET cc_start: 0.8116 (mmm) cc_final: 0.7619 (mmm) REVERT: E 439 GLU cc_start: 0.9125 (mp0) cc_final: 0.8359 (mp0) REVERT: F 207 MET cc_start: 0.8132 (mmm) cc_final: 0.7627 (mmm) REVERT: F 362 ASP cc_start: 0.8887 (t0) cc_final: 0.8625 (t70) REVERT: F 367 LEU cc_start: 0.9301 (mt) cc_final: 0.9014 (mm) REVERT: F 439 GLU cc_start: 0.9106 (mp0) cc_final: 0.8353 (mp0) REVERT: F 462 ASP cc_start: 0.8662 (m-30) cc_final: 0.8318 (m-30) REVERT: F 506 MET cc_start: 0.8967 (mtm) cc_final: 0.8744 (mtm) REVERT: G 17 ASP cc_start: 0.8496 (t0) cc_final: 0.8191 (t0) REVERT: G 75 PHE cc_start: 0.9047 (t80) cc_final: 0.8319 (t80) REVERT: G 164 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8120 (ttt) REVERT: G 231 GLU cc_start: 0.8741 (mp0) cc_final: 0.8481 (mp0) REVERT: G 298 ASP cc_start: 0.8941 (t0) cc_final: 0.8649 (t0) REVERT: H 17 ASP cc_start: 0.8500 (t0) cc_final: 0.8201 (t0) REVERT: H 75 PHE cc_start: 0.9024 (t80) cc_final: 0.8296 (t80) REVERT: H 164 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8103 (ttt) REVERT: H 231 GLU cc_start: 0.8736 (mp0) cc_final: 0.8468 (mp0) REVERT: H 290 VAL cc_start: 0.9393 (t) cc_final: 0.9139 (t) REVERT: I 99 THR cc_start: 0.6332 (OUTLIER) cc_final: 0.6054 (t) REVERT: I 206 CYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6370 (m) REVERT: J 156 ASP cc_start: 0.5894 (t0) cc_final: 0.4862 (p0) outliers start: 113 outliers final: 86 residues processed: 607 average time/residue: 0.3121 time to fit residues: 317.3537 Evaluate side-chains 618 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 525 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 196 MET Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 206 CYS Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 190 optimal weight: 7.9990 chunk 327 optimal weight: 30.0000 chunk 160 optimal weight: 5.9990 chunk 305 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 299 optimal weight: 20.0000 chunk 307 optimal weight: 0.0770 chunk 51 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 352 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.139555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109540 restraints weight = 48132.149| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.63 r_work: 0.3322 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 26213 Z= 0.267 Angle : 0.677 9.222 35599 Z= 0.368 Chirality : 0.047 0.189 4387 Planarity : 0.004 0.053 4526 Dihedral : 4.880 32.136 3615 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.45 % Allowed : 18.45 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3555 helix: 1.13 (0.14), residues: 1426 sheet: -1.38 (0.22), residues: 521 loop : -0.96 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 37 HIS 0.007 0.001 HIS G 128 PHE 0.023 0.002 PHE D 177 TYR 0.019 0.002 TYR B 128 ARG 0.001 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 1171) hydrogen bonds : angle 4.43785 ( 3315) covalent geometry : bond 0.00612 (26213) covalent geometry : angle 0.67696 (35599) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 534 time to evaluate : 3.645 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8321 (t0) cc_final: 0.7711 (t0) REVERT: A 270 ASP cc_start: 0.8601 (m-30) cc_final: 0.8174 (m-30) REVERT: A 276 LEU cc_start: 0.9199 (tp) cc_final: 0.8915 (tp) REVERT: B 50 ASP cc_start: 0.8361 (t0) cc_final: 0.7765 (t0) REVERT: B 106 LEU cc_start: 0.8812 (tt) cc_final: 0.8289 (tt) REVERT: B 295 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8422 (mt-10) REVERT: B 324 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: B 364 SER cc_start: 0.8911 (t) cc_final: 0.8709 (t) REVERT: C 20 GLU cc_start: 0.8914 (tt0) cc_final: 0.8110 (tp30) REVERT: C 32 GLU cc_start: 0.9051 (tt0) cc_final: 0.8059 (tm-30) REVERT: C 86 LEU cc_start: 0.9117 (tp) cc_final: 0.8887 (tt) REVERT: C 292 GLU cc_start: 0.8778 (tp30) cc_final: 0.8490 (tm-30) REVERT: C 293 GLU cc_start: 0.9124 (mp0) cc_final: 0.8875 (mp0) REVERT: C 303 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8766 (mp) REVERT: C 305 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8801 (mmtp) REVERT: D 156 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9127 (tt) REVERT: D 292 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8370 (tm-30) REVERT: D 303 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8726 (mp) REVERT: E 207 MET cc_start: 0.8105 (mmm) cc_final: 0.7723 (mmm) REVERT: E 257 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7923 (mmmt) REVERT: E 310 GLU cc_start: 0.8641 (pt0) cc_final: 0.8407 (pt0) REVERT: E 362 ASP cc_start: 0.8875 (t0) cc_final: 0.8612 (t70) REVERT: E 439 GLU cc_start: 0.9177 (mp0) cc_final: 0.8441 (mp0) REVERT: E 462 ASP cc_start: 0.8697 (m-30) cc_final: 0.8343 (m-30) REVERT: F 310 GLU cc_start: 0.8636 (pt0) cc_final: 0.8404 (pt0) REVERT: F 362 ASP cc_start: 0.8891 (t0) cc_final: 0.8626 (t70) REVERT: F 367 LEU cc_start: 0.9325 (mt) cc_final: 0.9004 (mm) REVERT: F 439 GLU cc_start: 0.9154 (mp0) cc_final: 0.8286 (mp0) REVERT: G 17 ASP cc_start: 0.8492 (t0) cc_final: 0.8119 (t0) REVERT: G 75 PHE cc_start: 0.9058 (t80) cc_final: 0.8338 (t80) REVERT: G 164 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8411 (ttt) REVERT: G 298 ASP cc_start: 0.9023 (t0) cc_final: 0.8753 (t0) REVERT: H 17 ASP cc_start: 0.8520 (t0) cc_final: 0.8165 (t0) REVERT: H 75 PHE cc_start: 0.9037 (t80) cc_final: 0.8336 (t80) REVERT: H 164 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8361 (ttt) REVERT: H 208 ASN cc_start: 0.8813 (t0) cc_final: 0.8608 (t0) REVERT: H 290 VAL cc_start: 0.9530 (t) cc_final: 0.9298 (t) REVERT: I 99 THR cc_start: 0.6384 (OUTLIER) cc_final: 0.6034 (t) REVERT: I 130 MET cc_start: 0.6632 (tmm) cc_final: 0.6425 (tmm) REVERT: I 161 ASP cc_start: 0.7629 (t70) cc_final: 0.7426 (t70) REVERT: I 183 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6976 (mtmt) REVERT: I 206 CYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6573 (m) outliers start: 137 outliers final: 102 residues processed: 605 average time/residue: 0.3303 time to fit residues: 334.7598 Evaluate side-chains 616 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 505 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 196 MET Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 206 CYS Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 261 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 292 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 333 GLN D 49 HIS D 154 GLN D 242 ASN E 234 GLN F 234 GLN J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.145523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115548 restraints weight = 47742.157| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.65 r_work: 0.3399 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26213 Z= 0.135 Angle : 0.561 8.501 35599 Z= 0.311 Chirality : 0.044 0.182 4387 Planarity : 0.004 0.051 4526 Dihedral : 4.431 32.136 3615 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.86 % Allowed : 21.03 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3555 helix: 1.50 (0.14), residues: 1424 sheet: -1.25 (0.22), residues: 534 loop : -0.81 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 37 HIS 0.008 0.001 HIS D 160 PHE 0.018 0.001 PHE C 177 TYR 0.011 0.001 TYR A 128 ARG 0.001 0.000 ARG H 74 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 1171) hydrogen bonds : angle 4.02484 ( 3315) covalent geometry : bond 0.00288 (26213) covalent geometry : angle 0.56056 (35599) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 573 time to evaluate : 2.943 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8209 (t0) cc_final: 0.7529 (t0) REVERT: A 106 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8213 (tt) REVERT: A 107 LEU cc_start: 0.8563 (tp) cc_final: 0.8268 (mp) REVERT: A 276 LEU cc_start: 0.9102 (tp) cc_final: 0.8792 (tp) REVERT: A 418 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6759 (mt-10) REVERT: A 423 VAL cc_start: 0.8826 (t) cc_final: 0.8586 (t) REVERT: B 50 ASP cc_start: 0.8239 (t0) cc_final: 0.7567 (t0) REVERT: B 106 LEU cc_start: 0.8768 (tt) cc_final: 0.8233 (tt) REVERT: B 167 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7788 (mm-30) REVERT: B 295 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8386 (mt-10) REVERT: B 418 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6859 (mt-10) REVERT: C 44 GLN cc_start: 0.7641 (tt0) cc_final: 0.7420 (tt0) REVERT: C 86 LEU cc_start: 0.9000 (tp) cc_final: 0.8748 (tt) REVERT: C 251 THR cc_start: 0.9047 (t) cc_final: 0.8793 (m) REVERT: C 293 GLU cc_start: 0.9127 (mp0) cc_final: 0.8917 (mp0) REVERT: C 303 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8695 (mp) REVERT: C 305 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8638 (mmtp) REVERT: D 251 THR cc_start: 0.9090 (t) cc_final: 0.8869 (m) REVERT: D 292 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8206 (tm-30) REVERT: D 303 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8692 (mp) REVERT: D 345 HIS cc_start: 0.8664 (OUTLIER) cc_final: 0.8062 (t-90) REVERT: E 207 MET cc_start: 0.7981 (mmm) cc_final: 0.7746 (mmm) REVERT: E 310 GLU cc_start: 0.8590 (pt0) cc_final: 0.8353 (pt0) REVERT: E 362 ASP cc_start: 0.8873 (t0) cc_final: 0.8623 (t70) REVERT: E 439 GLU cc_start: 0.9119 (mp0) cc_final: 0.8366 (mp0) REVERT: E 462 ASP cc_start: 0.8666 (m-30) cc_final: 0.8270 (m-30) REVERT: F 207 MET cc_start: 0.8011 (mmm) cc_final: 0.7767 (mmm) REVERT: F 295 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: F 310 GLU cc_start: 0.8599 (pt0) cc_final: 0.8357 (pt0) REVERT: F 362 ASP cc_start: 0.8902 (t0) cc_final: 0.8631 (t70) REVERT: F 367 LEU cc_start: 0.9321 (mt) cc_final: 0.9033 (mm) REVERT: F 439 GLU cc_start: 0.9098 (mp0) cc_final: 0.8339 (mp0) REVERT: F 462 ASP cc_start: 0.8687 (m-30) cc_final: 0.8328 (m-30) REVERT: G 17 ASP cc_start: 0.8463 (t0) cc_final: 0.8107 (t0) REVERT: G 70 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8553 (tp30) REVERT: G 164 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8175 (ttt) REVERT: G 298 ASP cc_start: 0.8923 (t0) cc_final: 0.8644 (t0) REVERT: H 17 ASP cc_start: 0.8494 (t0) cc_final: 0.8118 (t0) REVERT: H 164 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8712 (tpp) REVERT: H 290 VAL cc_start: 0.9414 (t) cc_final: 0.9179 (t) REVERT: H 298 ASP cc_start: 0.8863 (t0) cc_final: 0.8575 (t0) REVERT: I 183 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6888 (mtmt) REVERT: I 206 CYS cc_start: 0.6810 (m) cc_final: 0.6352 (m) REVERT: J 173 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7316 (tt0) REVERT: J 183 LYS cc_start: 0.7209 (mtpt) cc_final: 0.6659 (mtmt) outliers start: 97 outliers final: 69 residues processed: 619 average time/residue: 0.3124 time to fit residues: 322.6972 Evaluate side-chains 613 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 534 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 183 LYS Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 271 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 328 optimal weight: 20.0000 chunk 137 optimal weight: 0.0020 chunk 106 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS E 234 GLN F 234 GLN G 128 HIS J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.142889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112870 restraints weight = 48335.697| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.64 r_work: 0.3362 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26213 Z= 0.190 Angle : 0.610 10.429 35599 Z= 0.332 Chirality : 0.045 0.183 4387 Planarity : 0.004 0.050 4526 Dihedral : 4.486 31.794 3615 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.61 % Allowed : 21.55 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3555 helix: 1.54 (0.14), residues: 1418 sheet: -1.20 (0.22), residues: 535 loop : -0.83 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 37 HIS 0.010 0.001 HIS B 248 PHE 0.019 0.001 PHE D 177 TYR 0.011 0.001 TYR A 128 ARG 0.001 0.000 ARG L 52 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 1171) hydrogen bonds : angle 4.14372 ( 3315) covalent geometry : bond 0.00431 (26213) covalent geometry : angle 0.61043 (35599) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 531 time to evaluate : 3.281 Fit side-chains REVERT: A 50 ASP cc_start: 0.8294 (t0) cc_final: 0.7656 (t0) REVERT: A 106 LEU cc_start: 0.8800 (tt) cc_final: 0.8254 (tt) REVERT: A 270 ASP cc_start: 0.8645 (m-30) cc_final: 0.8296 (m-30) REVERT: A 276 LEU cc_start: 0.9141 (tp) cc_final: 0.8833 (tp) REVERT: A 418 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6787 (mt-10) REVERT: B 50 ASP cc_start: 0.8327 (t0) cc_final: 0.7712 (t0) REVERT: B 106 LEU cc_start: 0.8800 (tt) cc_final: 0.8255 (tt) REVERT: B 167 GLU cc_start: 0.8619 (mt-10) cc_final: 0.7869 (mm-30) REVERT: B 295 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8392 (mt-10) REVERT: C 20 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8171 (tp30) REVERT: C 86 LEU cc_start: 0.9078 (tp) cc_final: 0.8840 (tt) REVERT: C 175 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: C 251 THR cc_start: 0.9079 (t) cc_final: 0.8844 (m) REVERT: C 293 GLU cc_start: 0.9139 (mp0) cc_final: 0.8908 (mp0) REVERT: C 303 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8741 (mp) REVERT: C 305 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8719 (mmtp) REVERT: D 156 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9071 (tt) REVERT: D 251 THR cc_start: 0.9061 (t) cc_final: 0.8860 (m) REVERT: D 292 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8299 (tm-30) REVERT: D 303 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8693 (mp) REVERT: D 349 HIS cc_start: 0.9132 (m170) cc_final: 0.8745 (m90) REVERT: E 310 GLU cc_start: 0.8632 (pt0) cc_final: 0.8406 (pt0) REVERT: E 362 ASP cc_start: 0.8906 (t0) cc_final: 0.8650 (t70) REVERT: E 439 GLU cc_start: 0.9178 (mp0) cc_final: 0.8504 (mp0) REVERT: F 207 MET cc_start: 0.8064 (mmm) cc_final: 0.7713 (mmm) REVERT: F 295 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: F 310 GLU cc_start: 0.8644 (pt0) cc_final: 0.8405 (pt0) REVERT: F 362 ASP cc_start: 0.8893 (t0) cc_final: 0.8626 (t70) REVERT: F 367 LEU cc_start: 0.9327 (mt) cc_final: 0.9031 (mm) REVERT: F 439 GLU cc_start: 0.9146 (mp0) cc_final: 0.8422 (mp0) REVERT: F 462 ASP cc_start: 0.8687 (m-30) cc_final: 0.8281 (m-30) REVERT: G 17 ASP cc_start: 0.8464 (t0) cc_final: 0.8095 (t0) REVERT: G 70 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8580 (tp30) REVERT: G 164 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8218 (ttt) REVERT: G 208 ASN cc_start: 0.8708 (t0) cc_final: 0.8493 (t0) REVERT: G 298 ASP cc_start: 0.8971 (t0) cc_final: 0.8679 (t0) REVERT: H 17 ASP cc_start: 0.8522 (t0) cc_final: 0.8155 (t0) REVERT: H 164 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8180 (ttt) REVERT: H 290 VAL cc_start: 0.9457 (t) cc_final: 0.9238 (t) REVERT: H 298 ASP cc_start: 0.8912 (t0) cc_final: 0.8631 (t0) REVERT: I 206 CYS cc_start: 0.6931 (m) cc_final: 0.6502 (m) REVERT: J 183 LYS cc_start: 0.7262 (mtpt) cc_final: 0.6731 (mtmt) outliers start: 116 outliers final: 96 residues processed: 591 average time/residue: 0.3279 time to fit residues: 324.2750 Evaluate side-chains 625 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 520 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 196 MET Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 301 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 250 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 317 optimal weight: 20.0000 chunk 295 optimal weight: 0.2980 chunk 288 optimal weight: 20.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.142383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.112526 restraints weight = 48160.451| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.64 r_work: 0.3360 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26213 Z= 0.190 Angle : 0.613 9.146 35599 Z= 0.335 Chirality : 0.046 0.181 4387 Planarity : 0.004 0.050 4526 Dihedral : 4.542 31.346 3615 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.41 % Allowed : 20.83 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3555 helix: 1.50 (0.14), residues: 1427 sheet: -1.12 (0.23), residues: 515 loop : -0.83 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 37 HIS 0.008 0.001 HIS B 248 PHE 0.019 0.001 PHE D 177 TYR 0.014 0.001 TYR B 128 ARG 0.001 0.000 ARG H 102 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 1171) hydrogen bonds : angle 4.19029 ( 3315) covalent geometry : bond 0.00430 (26213) covalent geometry : angle 0.61269 (35599) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 532 time to evaluate : 3.287 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8312 (t0) cc_final: 0.7678 (t0) REVERT: A 106 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8226 (tt) REVERT: A 270 ASP cc_start: 0.8643 (m-30) cc_final: 0.8292 (m-30) REVERT: A 276 LEU cc_start: 0.9160 (tp) cc_final: 0.8831 (tp) REVERT: B 50 ASP cc_start: 0.8354 (t0) cc_final: 0.7746 (t0) REVERT: B 106 LEU cc_start: 0.8794 (tt) cc_final: 0.8242 (tt) REVERT: B 167 GLU cc_start: 0.8616 (mt-10) cc_final: 0.7900 (mm-30) REVERT: C 20 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8132 (tp30) REVERT: C 175 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: C 226 MET cc_start: 0.9196 (tpp) cc_final: 0.8993 (tpt) REVERT: C 293 GLU cc_start: 0.9147 (mp0) cc_final: 0.8906 (mp0) REVERT: C 303 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8760 (mp) REVERT: C 305 LYS cc_start: 0.9026 (mmmm) cc_final: 0.8775 (mmtp) REVERT: D 292 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8247 (tm-30) REVERT: D 303 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8712 (mp) REVERT: D 345 HIS cc_start: 0.8656 (OUTLIER) cc_final: 0.8139 (t-90) REVERT: D 349 HIS cc_start: 0.9123 (m170) cc_final: 0.8770 (m90) REVERT: E 207 MET cc_start: 0.8163 (mmm) cc_final: 0.7939 (mmm) REVERT: E 310 GLU cc_start: 0.8665 (pt0) cc_final: 0.8451 (pt0) REVERT: E 362 ASP cc_start: 0.8898 (t0) cc_final: 0.8645 (t70) REVERT: E 439 GLU cc_start: 0.9177 (mp0) cc_final: 0.8484 (mp0) REVERT: E 462 ASP cc_start: 0.8707 (m-30) cc_final: 0.8327 (m-30) REVERT: F 207 MET cc_start: 0.8083 (mmm) cc_final: 0.7708 (mmm) REVERT: F 295 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: F 310 GLU cc_start: 0.8655 (pt0) cc_final: 0.8443 (pt0) REVERT: F 362 ASP cc_start: 0.8874 (t0) cc_final: 0.8605 (t70) REVERT: F 367 LEU cc_start: 0.9349 (mt) cc_final: 0.9069 (mm) REVERT: F 439 GLU cc_start: 0.9184 (mp0) cc_final: 0.8459 (mp0) REVERT: F 462 ASP cc_start: 0.8725 (m-30) cc_final: 0.8422 (m-30) REVERT: G 17 ASP cc_start: 0.8482 (t0) cc_final: 0.8107 (t0) REVERT: G 70 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8532 (tp30) REVERT: G 164 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8263 (ttt) REVERT: G 208 ASN cc_start: 0.8764 (t0) cc_final: 0.8548 (t0) REVERT: G 298 ASP cc_start: 0.8973 (t0) cc_final: 0.8683 (t0) REVERT: H 17 ASP cc_start: 0.8484 (t0) cc_final: 0.8112 (t0) REVERT: H 70 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8528 (tp30) REVERT: H 164 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8163 (ttt) REVERT: H 298 ASP cc_start: 0.8913 (t0) cc_final: 0.8643 (t0) REVERT: I 206 CYS cc_start: 0.6982 (m) cc_final: 0.6535 (m) REVERT: J 183 LYS cc_start: 0.7265 (mtpt) cc_final: 0.6711 (mtmt) outliers start: 136 outliers final: 113 residues processed: 602 average time/residue: 0.3767 time to fit residues: 379.6199 Evaluate side-chains 639 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 517 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2834 > 50: distance: 49 - 73: 37.129 distance: 53 - 81: 33.170 distance: 60 - 86: 32.447 distance: 68 - 73: 34.427 distance: 69 - 94: 35.557 distance: 73 - 74: 57.033 distance: 74 - 75: 69.457 distance: 75 - 76: 57.695 distance: 75 - 81: 39.046 distance: 76 - 99: 40.490 distance: 77 - 78: 39.512 distance: 78 - 79: 56.671 distance: 78 - 80: 41.261 distance: 81 - 82: 54.410 distance: 82 - 83: 63.493 distance: 82 - 85: 38.536 distance: 83 - 84: 41.021 distance: 83 - 86: 51.767 distance: 84 - 104: 58.993 distance: 86 - 87: 40.966 distance: 87 - 88: 55.471 distance: 87 - 90: 56.150 distance: 88 - 89: 56.340 distance: 88 - 94: 57.822 distance: 89 - 113: 36.817 distance: 90 - 91: 21.791 distance: 91 - 92: 16.317 distance: 91 - 93: 60.557 distance: 94 - 95: 55.589 distance: 95 - 96: 68.757 distance: 95 - 98: 54.237 distance: 96 - 97: 45.708 distance: 96 - 99: 41.126 distance: 97 - 123: 57.589 distance: 99 - 100: 39.462 distance: 100 - 101: 40.883 distance: 100 - 103: 28.350 distance: 101 - 102: 39.388 distance: 104 - 105: 55.655 distance: 105 - 106: 67.296 distance: 105 - 108: 40.468 distance: 106 - 107: 67.872 distance: 106 - 113: 54.648 distance: 109 - 110: 38.856 distance: 110 - 111: 57.437 distance: 111 - 112: 40.732 distance: 113 - 114: 56.024 distance: 114 - 115: 53.148 distance: 114 - 117: 56.926 distance: 115 - 116: 40.664 distance: 115 - 123: 51.471 distance: 117 - 118: 68.032 distance: 118 - 119: 69.261 distance: 118 - 120: 70.580 distance: 119 - 121: 39.202 distance: 120 - 122: 55.358 distance: 121 - 122: 40.226 distance: 123 - 124: 57.913 distance: 124 - 125: 55.218 distance: 124 - 127: 56.235 distance: 125 - 126: 57.505 distance: 125 - 133: 39.204 distance: 127 - 128: 41.447 distance: 128 - 129: 55.391 distance: 128 - 130: 69.829 distance: 129 - 131: 57.720 distance: 130 - 132: 70.312 distance: 131 - 132: 55.251 distance: 133 - 134: 57.059 distance: 134 - 135: 38.818 distance: 134 - 137: 57.615 distance: 135 - 136: 57.488 distance: 135 - 139: 39.229 distance: 137 - 138: 41.502 distance: 140 - 141: 57.291 distance: 140 - 143: 39.664 distance: 141 - 142: 56.888 distance: 141 - 146: 33.660 distance: 143 - 145: 39.173