Starting phenix.real_space_refine on Sun Sep 13 14:11:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ecv_31058/09_2026/7ecv_31058.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ecv_31058/09_2026/7ecv_31058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ecv_31058/09_2026/7ecv_31058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ecv_31058/09_2026/7ecv_31058.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ecv_31058/09_2026/7ecv_31058.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ecv_31058/09_2026/7ecv_31058.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ecv_31058/09_2026/7ecv_31058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ecv_31058/09_2026/7ecv_31058.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 59 5.49 5 S 33 5.16 5 C 14826 2.51 5 N 4458 2.21 5 O 4777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24153 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1423 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 185, 1420 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 59 Conformer: "B" Number of residues, atoms: 185, 1420 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 59 bond proxies already assigned to first conformer: 1452 Chain: "A" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2065 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 309, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1402 Unresolved non-hydrogen angles: 2023 Unresolved non-hydrogen dihedrals: 916 Unresolved non-hydrogen chiralities: 389 Planarities with less than four sites: {'GLN:plan1': 28, 'GLU:plan': 24, 'ARG:plan': 32, 'PHE:plan': 11, 'ASP:plan': 21, 'HIS:plan': 11, 'TRP:plan': 9, 'ASN:plan1': 10, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 756 Chain: "B" Number of atoms: 2368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2368 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2265 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2548 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2560 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2574 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2560 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2547 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 318} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 122} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNAv2': 60} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 13, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 22, 'rna3p': 37} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.77, per 1000 atoms: 0.24 Number of scatterers: 24153 At special positions: 0 Unit cell: (154, 144.1, 140.8, 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 33 16.00 P 59 15.00 O 4777 8.00 N 4458 7.00 C 14826 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.2 seconds 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5196 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 42 sheets defined 31.7% alpha, 17.1% beta 0 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'L' and resid 16 through 36 Processing helix chain 'L' and resid 63 through 72 removed outlier: 3.933A pdb=" N ALA L 72 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.601A pdb=" N LEU L 76 " --> pdb=" O ARG L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 121 removed outlier: 3.920A pdb=" N LEU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 131 Processing helix chain 'L' and resid 132 through 136 removed outlier: 3.816A pdb=" N VAL L 135 " --> pdb=" O PRO L 132 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA L 136 " --> pdb=" O ASP L 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 132 through 136' Processing helix chain 'A' and resid 16 through 28 removed outlier: 4.422A pdb=" N PHE A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 51 through 63 removed outlier: 3.759A pdb=" N LEU A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 294 through 307 removed outlier: 4.091A pdb=" N LEU A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 5.754A pdb=" N ARG A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.621A pdb=" N VAL A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.512A pdb=" N LEU A 361 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TRP A 362 " --> pdb=" O GLU A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 362' Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.311A pdb=" N ARG A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.665A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 4.130A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.799A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.810A pdb=" N ALA B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.562A pdb=" N LEU B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.892A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 4.079A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.974A pdb=" N SER C 36 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 3.840A pdb=" N ARG C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 191 through 204 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 303 through 313 removed outlier: 3.697A pdb=" N ASP C 309 " --> pdb=" O TYR C 305 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 310 " --> pdb=" O THR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.594A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 removed outlier: 3.979A pdb=" N ILE D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 129 removed outlier: 3.720A pdb=" N LYS D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.909A pdb=" N ALA D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 304 through 313 Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 322 through 329 removed outlier: 4.136A pdb=" N VAL D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 327 " --> pdb=" O GLN D 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 removed outlier: 3.944A pdb=" N GLN E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.523A pdb=" N GLN E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 144 Processing helix chain 'E' and resid 191 through 204 removed outlier: 3.952A pdb=" N LEU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 263 removed outlier: 3.834A pdb=" N ALA E 263 " --> pdb=" O LYS E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 312 removed outlier: 3.884A pdb=" N LEU E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 4.143A pdb=" N HIS E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 Processing helix chain 'F' and resid 112 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 304 through 313 Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.689A pdb=" N GLY F 333 " --> pdb=" O ASN F 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 72 removed outlier: 3.766A pdb=" N ASP G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN G 72 " --> pdb=" O ASP G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.649A pdb=" N ARG G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 191 through 204 removed outlier: 3.990A pdb=" N LEU G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 removed outlier: 3.523A pdb=" N ALA G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 312 removed outlier: 4.423A pdb=" N ASP G 309 " --> pdb=" O TYR G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 removed outlier: 3.791A pdb=" N HIS G 324 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 72 removed outlier: 3.693A pdb=" N ASP H 68 " --> pdb=" O PRO H 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.753A pdb=" N ASN H 141 " --> pdb=" O ARG H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 204 Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 304 through 313 Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.200A pdb=" N ARG I 13 " --> pdb=" O ILE I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 30 removed outlier: 3.927A pdb=" N ALA I 30 " --> pdb=" O LYS I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 56 removed outlier: 3.511A pdb=" N ALA I 56 " --> pdb=" O GLU I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 75 removed outlier: 3.643A pdb=" N ALA I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 121 removed outlier: 3.644A pdb=" N LEU I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 13 removed outlier: 3.851A pdb=" N ARG J 13 " --> pdb=" O ILE J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 32 removed outlier: 4.234A pdb=" N ALA J 30 " --> pdb=" O LYS J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 56 Processing helix chain 'J' and resid 60 through 74 removed outlier: 3.800A pdb=" N ALA J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 121 removed outlier: 3.562A pdb=" N LEU J 113 " --> pdb=" O GLY J 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 41 through 43 Processing sheet with id=AA2, first strand: chain 'L' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'L' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'L' and resid 172 through 173 removed outlier: 4.171A pdb=" N GLY L 172 " --> pdb=" O LYS L 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 178 through 181 Processing sheet with id=AA7, first strand: chain 'A' and resid 178 through 181 removed outlier: 7.360A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 232 through 234 removed outlier: 4.468A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 219 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 234 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS B 217 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 240 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 263 through 264 removed outlier: 4.320A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 113 removed outlier: 3.738A pdb=" N ALA B 8 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 159 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.664A pdb=" N ARG B 65 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 12 through 14 removed outlier: 3.806A pdb=" N LEU C 12 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.567A pdb=" N VAL C 99 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL C 209 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.721A pdb=" N ALA C 23 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 255 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 229 through 230 removed outlier: 4.544A pdb=" N THR C 245 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 12 through 14 removed outlier: 3.584A pdb=" N GLY D 334 " --> pdb=" O PHE D 14 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.655A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.655A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA D 157 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 23 through 24 Processing sheet with id=AC2, first strand: chain 'D' and resid 44 through 51 Processing sheet with id=AC3, first strand: chain 'D' and resid 229 through 230 removed outlier: 4.738A pdb=" N THR D 245 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=AC5, first strand: chain 'E' and resid 170 through 177 removed outlier: 4.006A pdb=" N ARG E 172 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 44 through 49 removed outlier: 4.559A pdb=" N ALA E 82 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AC8, first strand: chain 'E' and resid 287 through 288 removed outlier: 3.562A pdb=" N LYS E 293 " --> pdb=" O VAL E 288 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.556A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 18 through 19 removed outlier: 4.096A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL F 158 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP F 177 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE F 162 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AD3, first strand: chain 'F' and resid 45 through 46 Processing sheet with id=AD4, first strand: chain 'F' and resid 49 through 51 removed outlier: 3.727A pdb=" N PHE I 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR I 102 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER I 96 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N PHE I 104 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS I 94 " --> pdb=" O PHE I 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 287 through 288 removed outlier: 3.524A pdb=" N VAL F 288 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 293 " --> pdb=" O VAL F 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'G' and resid 108 through 109 removed outlier: 3.565A pdb=" N ALA G 108 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 18 through 20 removed outlier: 4.097A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 18 through 20 Processing sheet with id=AD9, first strand: chain 'G' and resid 44 through 51 removed outlier: 7.076A pdb=" N LYS G 242 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR G 78 " --> pdb=" O LYS G 242 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS G 244 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 287 through 288 removed outlier: 3.749A pdb=" N VAL G 288 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS G 293 " --> pdb=" O VAL G 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'H' and resid 108 through 109 Processing sheet with id=AE3, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.505A pdb=" N ARG H 98 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.505A pdb=" N ARG H 98 " --> pdb=" O ASP H 19 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 44 through 51 removed outlier: 4.200A pdb=" N ALA H 82 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 44 through 51 removed outlier: 8.178A pdb=" N THR H 78 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 11.811A pdb=" N CYS J 106 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 15.211A pdb=" N ASP H 80 " --> pdb=" O CYS J 106 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE J 92 " --> pdb=" O TYR J 105 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2622 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6173 1.33 - 1.45: 5105 1.45 - 1.57: 13283 1.57 - 1.69: 118 1.69 - 1.81: 50 Bond restraints: 24729 Sorted by residual: bond pdb=" CA ASN E 75 " pdb=" C ASN E 75 " ideal model delta sigma weight residual 1.526 1.492 0.034 1.08e-02 8.57e+03 9.72e+00 bond pdb=" C TYR F 271 " pdb=" N PRO F 272 " ideal model delta sigma weight residual 1.335 1.375 -0.040 1.38e-02 5.25e+03 8.44e+00 bond pdb=" N ASN H 75 " pdb=" CA ASN H 75 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.58e+00 bond pdb=" CG1 ILE E 260 " pdb=" CD1 ILE E 260 " ideal model delta sigma weight residual 1.513 1.425 0.088 3.90e-02 6.57e+02 5.13e+00 bond pdb=" C TYR B 262 " pdb=" N LEU B 263 " ideal model delta sigma weight residual 1.329 1.262 0.067 3.03e-02 1.09e+03 4.91e+00 ... (remaining 24724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 32164 1.97 - 3.94: 1303 3.94 - 5.90: 180 5.90 - 7.87: 33 7.87 - 9.84: 11 Bond angle restraints: 33691 Sorted by residual: angle pdb=" N LEU B 139 " pdb=" CA LEU B 139 " pdb=" C LEU B 139 " ideal model delta sigma weight residual 113.38 122.15 -8.77 1.23e+00 6.61e-01 5.08e+01 angle pdb=" N ILE D 267 " pdb=" CA ILE D 267 " pdb=" C ILE D 267 " ideal model delta sigma weight residual 112.83 118.95 -6.12 9.90e-01 1.02e+00 3.82e+01 angle pdb=" C ILE D 267 " pdb=" N ASP D 268 " pdb=" CA ASP D 268 " ideal model delta sigma weight residual 123.05 115.48 7.57 1.40e+00 5.10e-01 2.92e+01 angle pdb=" C GLN E 241 " pdb=" CA GLN E 241 " pdb=" CB GLN E 241 " ideal model delta sigma weight residual 116.54 111.04 5.50 1.15e+00 7.56e-01 2.28e+01 angle pdb=" N VAL E 249 " pdb=" CA VAL E 249 " pdb=" C VAL E 249 " ideal model delta sigma weight residual 109.34 100.85 8.49 2.08e+00 2.31e-01 1.67e+01 ... (remaining 33686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.03: 13589 32.03 - 64.05: 597 64.05 - 96.08: 76 96.08 - 128.11: 0 128.11 - 160.13: 1 Dihedral angle restraints: 14263 sinusoidal: 5883 harmonic: 8380 Sorted by residual: dihedral pdb=" C4' A M 3 " pdb=" C3' A M 3 " pdb=" C2' A M 3 " pdb=" C1' A M 3 " ideal model delta sinusoidal sigma weight residual 36.34 -38.60 74.94 1 3.10e+00 1.04e-01 7.39e+02 dihedral pdb=" C4' C M 58 " pdb=" C3' C M 58 " pdb=" C2' C M 58 " pdb=" C1' C M 58 " ideal model delta sinusoidal sigma weight residual 36.34 -37.13 73.48 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' G M 60 " pdb=" C3' G M 60 " pdb=" C2' G M 60 " pdb=" C1' G M 60 " ideal model delta sinusoidal sigma weight residual 36.34 -36.84 73.19 1 3.10e+00 1.04e-01 7.10e+02 ... (remaining 14260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3011 0.071 - 0.143: 442 0.143 - 0.214: 79 0.214 - 0.286: 75 0.286 - 0.357: 10 Chirality restraints: 3617 Sorted by residual: chirality pdb=" P A M 59 " pdb=" OP1 A M 59 " pdb=" OP2 A M 59 " pdb=" O5' A M 59 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA LEU B 139 " pdb=" N LEU B 139 " pdb=" C LEU B 139 " pdb=" CB LEU B 139 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C2' C M 13 " pdb=" C3' C M 13 " pdb=" O2' C M 13 " pdb=" C1' C M 13 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3614 not shown) Planarity restraints: 4314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR F 271 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO F 272 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO F 272 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 272 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 266 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C THR D 266 " 0.044 2.00e-02 2.50e+03 pdb=" O THR D 266 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE D 267 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG L 73 " -0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO L 74 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO L 74 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO L 74 " -0.034 5.00e-02 4.00e+02 ... (remaining 4311 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 110 2.44 - 3.05: 13553 3.05 - 3.67: 35980 3.67 - 4.28: 52622 4.28 - 4.90: 89070 Nonbonded interactions: 191335 Sorted by model distance: nonbonded pdb=" CE1 TYR A 179 " pdb=" CD1 LEU A 189 " model vdw 1.821 3.760 nonbonded pdb=" O ASP D 303 " pdb=" CD2 LEU D 307 " model vdw 1.834 3.460 nonbonded pdb=" OD1 ASP D 303 " pdb=" N TYR D 305 " model vdw 1.905 3.120 nonbonded pdb=" OD1 ASP D 303 " pdb=" N PHE D 304 " model vdw 2.028 3.120 nonbonded pdb=" O4' C M 58 " pdb=" OP2 A M 59 " model vdw 2.048 3.040 ... (remaining 191330 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 'C' and (resid 6 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 211 or (resid 212 and (name N or na \ me CA or name C or name O or name CB )) or resid 213 through 249 or (resid 250 a \ nd (name N or name CA or name C or name O or name CB )) or resid 251 through 272 \ or (resid 273 through 275 and (name N or name CA or name C or name O or name CB \ )) or resid 276 through 282 or (resid 283 and (name N or name CA or name C or n \ ame O or name CB )) or resid 284 through 336)) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 211 or (resid 212 and (na \ me N or name CA or name C or name O or name CB )) or resid 213 through 231 or re \ sid 244 through 282 or (resid 283 and (name N or name CA or name C or name O or \ name CB )) or resid 284 through 292 or (resid 293 through 294 and (name N or nam \ e CA or name C or name O or name CB )) or resid 295 through 302 or (resid 303 an \ d (name N or name CA or name C or name O or name CB )) or resid 304 through 306 \ or (resid 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 through 336)) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 79 or (resid 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 through 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 231 or resid 244 through 249 or (resid 250 and (name N or name CA or name C \ or name O or name CB )) or resid 251 through 292 or (resid 293 through 294 and ( \ name N or name CA or name C or name O or name CB )) or resid 295 through 302 or \ (resid 303 and (name N or name CA or name C or name O or name CB )) or resid 304 \ through 306 or (resid 307 and (name N or name CA or name C or name O or name CB \ )) or resid 308 through 336)) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 79 or (resid 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 through 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 231 or resid 244 through 249 or (resid 250 and (name N or name CA or name C \ or name O or name CB )) or resid 251 through 282 or (resid 283 and (name N or na \ me CA or name C or name O or name CB )) or resid 284 through 292 or (resid 293 t \ hrough 294 and (name N or name CA or name C or name O or name CB )) or resid 295 \ through 302 or (resid 303 and (name N or name CA or name C or name O or name CB \ )) or resid 304 through 306 or (resid 307 and (name N or name CA or name C or n \ ame O or name CB )) or resid 308 through 336)) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 79 or (resid 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 through 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 231 or resid 244 through 249 or (resid 250 and (name N or name CA or name C \ or name O or name CB )) or resid 251 through 282 or (resid 283 and (name N or na \ me CA or name C or name O or name CB )) or resid 284 through 292 or (resid 293 t \ hrough 294 and (name N or name CA or name C or name O or name CB )) or resid 295 \ through 302 or (resid 303 and (name N or name CA or name C or name O or name CB \ )) or resid 304 through 306 or (resid 307 and (name N or name CA or name C or n \ ame O or name CB )) or resid 308 through 336)) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 79 or (resid 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 through 231 or resid \ 244 through 249 or (resid 250 and (name N or name CA or name C or name O or nam \ e CB )) or resid 251 through 292 or (resid 293 through 294 and (name N or name C \ A or name C or name O or name CB )) or resid 295 through 302 or (resid 303 and ( \ name N or name CA or name C or name O or name CB )) or resid 304 through 306 or \ (resid 307 and (name N or name CA or name C or name O or name CB )) or resid 308 \ through 336)) } ncs_group { reference = (chain 'I' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 30 or (resid 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 through 46 or (resid 47 and (n \ ame N or name CA or name C or name O or name CB )) or resid 48 through 50 or (re \ sid 51 and (name N or name CA or name C or name O or name CB )) or resid 52 thro \ ugh 62 or (resid 63 through 64 and (name N or name CA or name C or name O or nam \ e CB )) or resid 65 through 124)) selection = (chain 'J' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 through 124)) } 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=0.37 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.750 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.006 0.388 24730 Z= 0.367 Angle : 0.900 9.841 33691 Z= 0.488 Chirality : 0.066 0.357 3617 Planarity : 0.006 0.067 4314 Dihedral : 17.444 160.134 9067 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.40 % Rotamer: Outliers : 0.87 % Allowed : 14.05 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.12), residues: 3092 helix: -2.79 (0.12), residues: 940 sheet: -1.72 (0.22), residues: 510 loop : -3.09 (0.12), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 111 TYR 0.021 0.002 TYR E 247 PHE 0.021 0.002 PHE G 95 TRP 0.015 0.002 TRP A 263 HIS 0.011 0.002 HIS L 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.27 (24729) covalent geometry : angle 0.90041 / 0.49 (33691) hydrogen bonds : bond 0.14006 / 9.90 ( 902) hydrogen bonds : angle 6.93222 / 4.89 ( 2622) Misc. bond : bond 0.38794 / 20.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 447 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7074 (pt0) cc_final: 0.6854 (pt0) REVERT: B 131 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7148 (tm-30) REVERT: B 258 LEU cc_start: 0.8139 (pt) cc_final: 0.7853 (pp) REVERT: C 140 HIS cc_start: 0.7342 (m-70) cc_final: 0.7038 (t-90) REVERT: C 283 GLU cc_start: 0.7226 (tp30) cc_final: 0.6957 (tp30) REVERT: D 303 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7486 (p0) REVERT: E 302 LEU cc_start: 0.8637 (mt) cc_final: 0.8316 (mp) REVERT: E 322 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: H 89 ASP cc_start: 0.7989 (t70) cc_final: 0.7699 (t0) REVERT: H 244 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8289 (ttpp) REVERT: I 7 ILE cc_start: 0.7076 (mm) cc_final: 0.6701 (mm) REVERT: I 8 GLU cc_start: 0.7456 (pp20) cc_final: 0.6848 (pp20) outliers start: 19 outliers final: 13 residues processed: 461 average time/residue: 0.2077 time to fit residues: 140.9425 Evaluate side-chains 348 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 333 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.0980 chunk 298 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 108 ASN L 165 GLN A 177 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN A 230 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN B 64 HIS B 69 GLN B 82 ASN B 89 ASN B 104 HIS B 114 HIS B 172 ASN B 173 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 163 ASN D 164 HIS E 110 ASN E 127 ASN E 163 ASN E 208 HIS E 223 GLN F 83 ASN F 163 ASN F 208 HIS G 163 ASN G 310 ASN G 322 GLN H 77 GLN H 167 GLN H 208 HIS H 223 GLN H 310 ASN H 329 ASN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN J 55 GLN J 120 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.181633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.141855 restraints weight = 34510.978| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 4.22 r_work: 0.3070 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24730 Z= 0.149 Angle : 0.797 15.118 33691 Z= 0.362 Chirality : 0.066 1.052 3617 Planarity : 0.004 0.057 4314 Dihedral : 11.888 162.640 4128 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 3.42 % Allowed : 17.06 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.13), residues: 3092 helix: -0.92 (0.16), residues: 965 sheet: -1.35 (0.23), residues: 501 loop : -2.71 (0.13), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 175 TYR 0.015 0.001 TYR I 95 PHE 0.018 0.001 PHE C 304 TRP 0.013 0.001 TRP C 39 HIS 0.006 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (24729) covalent geometry : angle 0.79747 / 0.36 (33691) hydrogen bonds : bond 0.03565 / 2.44 ( 902) hydrogen bonds : angle 4.97474 / 3.53 ( 2622) Misc. bond : bond 0.00077 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 362 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8697 (mp) REVERT: B 82 ASN cc_start: 0.8934 (m-40) cc_final: 0.8621 (m-40) REVERT: B 169 ARG cc_start: 0.5017 (mtt90) cc_final: 0.4791 (mmt90) REVERT: B 301 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8215 (pp) REVERT: C 15 GLU cc_start: 0.7851 (mp0) cc_final: 0.7632 (mp0) REVERT: C 131 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.6928 (p90) REVERT: E 50 ARG cc_start: 0.8528 (ptt180) cc_final: 0.8322 (ptt180) REVERT: E 264 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8823 (mt) REVERT: E 322 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7789 (mt0) REVERT: F 50 ARG cc_start: 0.8549 (ttt180) cc_final: 0.8148 (ttp-170) REVERT: F 172 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7434 (ptm160) REVERT: F 237 ASP cc_start: 0.7775 (m-30) cc_final: 0.7433 (t0) REVERT: F 283 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7753 (tt0) REVERT: G 19 ASP cc_start: 0.8357 (t0) cc_final: 0.8137 (t0) REVERT: G 309 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8033 (p0) REVERT: H 75 ASN cc_start: 0.9387 (OUTLIER) cc_final: 0.9159 (p0) REVERT: H 89 ASP cc_start: 0.8438 (t70) cc_final: 0.7810 (t0) REVERT: I 8 GLU cc_start: 0.7132 (pp20) cc_final: 0.6651 (pp20) REVERT: I 9 ILE cc_start: 0.8171 (mt) cc_final: 0.7414 (mt) REVERT: I 12 ASN cc_start: 0.8990 (p0) cc_final: 0.8738 (p0) REVERT: I 120 ASN cc_start: 0.8126 (m110) cc_final: 0.7522 (m110) REVERT: J 73 LYS cc_start: 0.8252 (pttp) cc_final: 0.8007 (pttp) REVERT: J 81 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8116 (mm-30) REVERT: J 122 ARG cc_start: 0.7898 (tpt170) cc_final: 0.7614 (tmt-80) outliers start: 75 outliers final: 44 residues processed: 412 average time/residue: 0.1929 time to fit residues: 119.3697 Evaluate side-chains 359 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 309 ASP Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain I residue 77 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 68 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 199 optimal weight: 0.0040 chunk 119 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 89 ASN B 114 HIS B 172 ASN C 77 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN E 127 ASN E 291 GLN F 329 ASN H 167 GLN H 329 ASN I 21 HIS I 53 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.176951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148862 restraints weight = 40390.854| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.85 r_work: 0.3075 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24730 Z= 0.187 Angle : 0.720 12.468 33691 Z= 0.340 Chirality : 0.057 0.714 3617 Planarity : 0.004 0.048 4314 Dihedral : 11.588 165.946 4114 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.62 % Rotamer: Outliers : 4.11 % Allowed : 18.75 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.14), residues: 3092 helix: -0.07 (0.17), residues: 953 sheet: -1.12 (0.23), residues: 500 loop : -2.46 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 189 TYR 0.016 0.002 TYR J 89 PHE 0.017 0.001 PHE G 95 TRP 0.013 0.001 TRP C 30 HIS 0.008 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (24729) covalent geometry : angle 0.72023 / 0.34 (33691) hydrogen bonds : bond 0.03475 / 2.38 ( 902) hydrogen bonds : angle 4.72167 / 3.36 ( 2622) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 323 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8611 (mp) REVERT: B 169 ARG cc_start: 0.5305 (mtt90) cc_final: 0.5071 (mmt90) REVERT: B 301 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8199 (pp) REVERT: B 313 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8435 (mp) REVERT: C 30 TRP cc_start: 0.6086 (t-100) cc_final: 0.5341 (m100) REVERT: C 131 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7138 (p90) REVERT: C 141 ASN cc_start: 0.6944 (m110) cc_final: 0.6531 (m110) REVERT: C 329 ASN cc_start: 0.8595 (t0) cc_final: 0.7600 (t0) REVERT: D 49 VAL cc_start: 0.8535 (p) cc_final: 0.8315 (m) REVERT: E 166 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7631 (tpp80) REVERT: E 175 ARG cc_start: 0.8345 (tpp80) cc_final: 0.8106 (ttm170) REVERT: E 264 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8805 (mt) REVERT: E 322 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: F 172 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7500 (ptm160) REVERT: F 237 ASP cc_start: 0.7714 (m-30) cc_final: 0.7505 (t0) REVERT: G 300 GLN cc_start: 0.7905 (mp10) cc_final: 0.7615 (mp10) REVERT: H 75 ASN cc_start: 0.9412 (OUTLIER) cc_final: 0.9139 (p0) REVERT: H 89 ASP cc_start: 0.8508 (t70) cc_final: 0.7977 (t0) REVERT: I 8 GLU cc_start: 0.7472 (pp20) cc_final: 0.6942 (pp20) REVERT: I 9 ILE cc_start: 0.8310 (mt) cc_final: 0.7612 (mt) REVERT: I 120 ASN cc_start: 0.8207 (m110) cc_final: 0.7669 (m110) REVERT: J 29 ASN cc_start: 0.6070 (m-40) cc_final: 0.5558 (m110) REVERT: J 81 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8182 (mm-30) outliers start: 90 outliers final: 49 residues processed: 381 average time/residue: 0.1892 time to fit residues: 108.9529 Evaluate side-chains 355 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 298 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 301 LYS Chi-restraints excluded: chain I residue 77 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 57 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 249 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 80 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 69 GLN B 114 HIS B 172 ASN C 77 GLN C 164 HIS ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN E 127 ASN H 167 GLN H 329 ASN J 53 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.180569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.145302 restraints weight = 40267.962| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.45 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24730 Z= 0.108 Angle : 0.642 12.785 33691 Z= 0.301 Chirality : 0.049 0.509 3617 Planarity : 0.004 0.044 4314 Dihedral : 11.369 165.963 4112 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.56 % Rotamer: Outliers : 3.38 % Allowed : 20.12 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.15), residues: 3092 helix: 0.42 (0.17), residues: 966 sheet: -0.86 (0.24), residues: 465 loop : -2.25 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 150 TYR 0.014 0.001 TYR I 95 PHE 0.013 0.001 PHE B 152 TRP 0.011 0.001 TRP B 316 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (24729) covalent geometry : angle 0.64216 / 0.30 (33691) hydrogen bonds : bond 0.02897 / 1.99 ( 902) hydrogen bonds : angle 4.40582 / 3.12 ( 2622) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 343 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.3339 (OUTLIER) cc_final: 0.2985 (mtp) REVERT: L 10 ARG cc_start: 0.5717 (tpp80) cc_final: 0.5323 (ttp-170) REVERT: A 178 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8281 (mp) REVERT: A 207 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7691 (ttm170) REVERT: B 301 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8074 (pp) REVERT: C 30 TRP cc_start: 0.5862 (t-100) cc_final: 0.5520 (m100) REVERT: C 131 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.7061 (p90) REVERT: C 141 ASN cc_start: 0.6625 (m110) cc_final: 0.6387 (m110) REVERT: D 50 ARG cc_start: 0.7339 (ttp80) cc_final: 0.7013 (ttp-110) REVERT: E 264 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8536 (mt) REVERT: G 156 GLU cc_start: 0.7879 (tt0) cc_final: 0.7652 (tt0) REVERT: G 219 ILE cc_start: 0.8856 (mm) cc_final: 0.8643 (mt) REVERT: H 75 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8797 (p0) REVERT: H 89 ASP cc_start: 0.7977 (t70) cc_final: 0.7531 (t0) REVERT: H 91 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8757 (tp) REVERT: H 293 LYS cc_start: 0.7794 (ttmt) cc_final: 0.7199 (mtpt) REVERT: I 8 GLU cc_start: 0.7107 (pp20) cc_final: 0.6510 (pp20) REVERT: I 9 ILE cc_start: 0.8075 (mt) cc_final: 0.7358 (mt) REVERT: I 120 ASN cc_start: 0.8189 (m110) cc_final: 0.7869 (m110) REVERT: J 29 ASN cc_start: 0.5480 (m-40) cc_final: 0.5193 (m110) REVERT: J 73 LYS cc_start: 0.7378 (pttp) cc_final: 0.6597 (ptmt) REVERT: J 76 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6450 (tttt) outliers start: 74 outliers final: 38 residues processed: 384 average time/residue: 0.1798 time to fit residues: 105.4918 Evaluate side-chains 344 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 301 LYS Chi-restraints excluded: chain J residue 76 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 248 optimal weight: 0.1980 chunk 55 optimal weight: 40.0000 chunk 27 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 252 optimal weight: 0.9990 chunk 51 optimal weight: 50.0000 chunk 120 optimal weight: 7.9990 chunk 309 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS C 163 ASN C 329 ASN E 127 ASN H 167 GLN ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 120 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.175552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.144274 restraints weight = 39993.795| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.11 r_work: 0.3019 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 24730 Z= 0.249 Angle : 0.761 13.957 33691 Z= 0.359 Chirality : 0.058 0.683 3617 Planarity : 0.004 0.042 4314 Dihedral : 11.543 165.870 4107 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.25 % Favored : 91.72 % Rotamer: Outliers : 4.24 % Allowed : 21.03 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.15), residues: 3092 helix: 0.50 (0.17), residues: 950 sheet: -0.71 (0.24), residues: 464 loop : -2.28 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 166 TYR 0.022 0.002 TYR E 247 PHE 0.020 0.002 PHE H 95 TRP 0.012 0.001 TRP E 30 HIS 0.010 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 (24729) covalent geometry : angle 0.76140 / 0.36 (33691) hydrogen bonds : bond 0.03607 / 2.45 ( 902) hydrogen bonds : angle 4.67928 / 3.32 ( 2622) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 299 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.3706 (mtm) cc_final: 0.3455 (mtp) REVERT: L 10 ARG cc_start: 0.5416 (tpp80) cc_final: 0.4700 (ttp-170) REVERT: A 178 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 207 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.8053 (ttm170) REVERT: B 105 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8453 (pp) REVERT: B 301 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8276 (pp) REVERT: B 313 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8525 (mp) REVERT: C 77 GLN cc_start: 0.4635 (OUTLIER) cc_final: 0.4021 (mp10) REVERT: C 131 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.6985 (p90) REVERT: D 50 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7161 (ttp-110) REVERT: E 175 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7996 (ttm170) REVERT: E 231 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8140 (tp) REVERT: E 264 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8739 (mt) REVERT: F 172 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7327 (ptm160) REVERT: G 300 GLN cc_start: 0.7935 (mp10) cc_final: 0.7660 (mp10) REVERT: H 75 ASN cc_start: 0.9481 (OUTLIER) cc_final: 0.9218 (p0) REVERT: H 89 ASP cc_start: 0.8590 (t70) cc_final: 0.8086 (t0) REVERT: H 91 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8618 (tp) REVERT: I 6 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6774 (mmm) REVERT: I 8 GLU cc_start: 0.7495 (pp20) cc_final: 0.6923 (pp20) REVERT: I 9 ILE cc_start: 0.8355 (mt) cc_final: 0.7496 (mt) REVERT: I 69 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7412 (mt-10) REVERT: I 120 ASN cc_start: 0.8187 (m110) cc_final: 0.7629 (m110) REVERT: J 6 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7568 (mmt) REVERT: J 29 ASN cc_start: 0.6110 (m-40) cc_final: 0.5644 (m110) REVERT: J 122 ARG cc_start: 0.7974 (tmt-80) cc_final: 0.7751 (tmt-80) outliers start: 93 outliers final: 54 residues processed: 365 average time/residue: 0.1821 time to fit residues: 101.8293 Evaluate side-chains 347 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 280 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 6 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 303 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 112 optimal weight: 0.0060 chunk 254 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 22 optimal weight: 50.0000 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 64 HIS B 114 HIS C 77 GLN C 141 ASN D 141 ASN E 127 ASN H 167 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.182724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.150235 restraints weight = 39730.170| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.11 r_work: 0.3136 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24730 Z= 0.114 Angle : 0.640 11.016 33691 Z= 0.302 Chirality : 0.049 0.465 3617 Planarity : 0.003 0.043 4314 Dihedral : 11.245 164.445 4107 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.56 % Allowed : 22.26 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 3092 helix: 0.87 (0.18), residues: 947 sheet: -0.48 (0.25), residues: 454 loop : -2.07 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 166 TYR 0.014 0.001 TYR I 95 PHE 0.014 0.001 PHE B 152 TRP 0.016 0.001 TRP C 30 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (24729) covalent geometry : angle 0.63969 / 0.30 (33691) hydrogen bonds : bond 0.02886 / 1.97 ( 902) hydrogen bonds : angle 4.36945 / 3.09 ( 2622) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 312 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.3539 (mtm) cc_final: 0.2651 (ttm) REVERT: L 10 ARG cc_start: 0.5422 (tpp80) cc_final: 0.4605 (ttp-170) REVERT: A 176 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7880 (mmtt) REVERT: A 178 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 207 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.8014 (ttm170) REVERT: C 131 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6920 (p90) REVERT: C 141 ASN cc_start: 0.6781 (m-40) cc_final: 0.6528 (m110) REVERT: C 259 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7999 (tptt) REVERT: D 50 ARG cc_start: 0.7569 (ttp80) cc_final: 0.7030 (ttp-110) REVERT: E 231 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8205 (tp) REVERT: E 264 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8669 (mt) REVERT: F 172 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7324 (ptm160) REVERT: H 89 ASP cc_start: 0.8443 (t70) cc_final: 0.7963 (t0) REVERT: H 91 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8855 (tp) REVERT: I 8 GLU cc_start: 0.7384 (pp20) cc_final: 0.6785 (pp20) REVERT: I 9 ILE cc_start: 0.8313 (mt) cc_final: 0.7510 (mt) REVERT: I 69 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7153 (mt-10) REVERT: I 120 ASN cc_start: 0.8143 (m110) cc_final: 0.7658 (m110) REVERT: J 6 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7749 (mmt) REVERT: J 73 LYS cc_start: 0.8139 (pttp) cc_final: 0.7738 (pttp) REVERT: J 119 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7747 (tm-30) REVERT: J 122 ARG cc_start: 0.7775 (tmt-80) cc_final: 0.7535 (tmt-80) outliers start: 78 outliers final: 45 residues processed: 364 average time/residue: 0.1831 time to fit residues: 102.2162 Evaluate side-chains 350 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 298 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 301 LYS Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 6 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 260 optimal weight: 4.9990 chunk 243 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 167 optimal weight: 0.2980 chunk 193 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 228 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 266 optimal weight: 0.7980 chunk 272 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 114 HIS C 77 GLN E 127 ASN F 229 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 322 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.184041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.148525 restraints weight = 31831.479| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.93 r_work: 0.3243 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24730 Z= 0.098 Angle : 0.623 13.363 33691 Z= 0.291 Chirality : 0.047 0.317 3617 Planarity : 0.004 0.042 4314 Dihedral : 11.073 163.201 4105 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.28 % Allowed : 22.72 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.15), residues: 3092 helix: 1.02 (0.18), residues: 968 sheet: -0.38 (0.25), residues: 461 loop : -1.99 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 184 TYR 0.015 0.001 TYR I 95 PHE 0.014 0.001 PHE B 152 TRP 0.015 0.001 TRP C 30 HIS 0.004 0.001 HIS G 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (24729) covalent geometry : angle 0.62329 / 0.29 (33691) hydrogen bonds : bond 0.02643 / 1.80 ( 902) hydrogen bonds : angle 4.19390 / 2.95 ( 2622) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 348 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.3259 (mtm) cc_final: 0.2436 (ttm) REVERT: L 10 ARG cc_start: 0.5695 (tpp80) cc_final: 0.4768 (ttp-170) REVERT: A 178 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8201 (mp) REVERT: A 207 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7992 (ttm170) REVERT: C 77 GLN cc_start: 0.3595 (OUTLIER) cc_final: 0.3307 (mt0) REVERT: C 131 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6699 (p90) REVERT: C 141 ASN cc_start: 0.6355 (m-40) cc_final: 0.6081 (m110) REVERT: D 50 ARG cc_start: 0.7245 (ttp80) cc_final: 0.6842 (ttp-110) REVERT: E 175 ARG cc_start: 0.8081 (tpp80) cc_final: 0.7796 (tpp80) REVERT: E 302 LEU cc_start: 0.8638 (mt) cc_final: 0.8355 (mp) REVERT: F 50 ARG cc_start: 0.8551 (ttt180) cc_final: 0.8281 (ttp-170) REVERT: F 61 ASP cc_start: 0.7097 (t70) cc_final: 0.6847 (t0) REVERT: F 172 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7268 (ptm160) REVERT: G 219 ILE cc_start: 0.9071 (mm) cc_final: 0.8758 (mt) REVERT: H 83 ASN cc_start: 0.8692 (m-40) cc_final: 0.8474 (m-40) REVERT: H 89 ASP cc_start: 0.8126 (t70) cc_final: 0.7628 (t0) REVERT: I 6 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6731 (mmm) REVERT: I 8 GLU cc_start: 0.7228 (pp20) cc_final: 0.6628 (pp20) REVERT: I 9 ILE cc_start: 0.8273 (mt) cc_final: 0.7435 (mt) REVERT: I 69 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7111 (mt-10) REVERT: I 120 ASN cc_start: 0.8200 (m110) cc_final: 0.7736 (m110) REVERT: J 6 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7605 (mmt) REVERT: J 73 LYS cc_start: 0.8111 (pttp) cc_final: 0.7725 (pttp) REVERT: J 119 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7648 (tm-30) outliers start: 72 outliers final: 42 residues processed: 393 average time/residue: 0.1785 time to fit residues: 106.8110 Evaluate side-chains 362 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 38 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 174 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 114 HIS C 77 GLN E 127 ASN E 291 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.179777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.148221 restraints weight = 39957.060| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.02 r_work: 0.3120 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24730 Z= 0.157 Angle : 0.672 13.681 33691 Z= 0.315 Chirality : 0.050 0.381 3617 Planarity : 0.004 0.041 4314 Dihedral : 11.154 162.460 4105 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.06 % Allowed : 23.49 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 3092 helix: 1.06 (0.18), residues: 953 sheet: -0.42 (0.24), residues: 497 loop : -1.91 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 184 TYR 0.020 0.001 TYR I 95 PHE 0.015 0.001 PHE G 95 TRP 0.011 0.001 TRP A 263 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (24729) covalent geometry : angle 0.67218 / 0.31 (33691) hydrogen bonds : bond 0.02979 / 2.04 ( 902) hydrogen bonds : angle 4.29467 / 3.03 ( 2622) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 294 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5669 (tpp80) cc_final: 0.4740 (ttp-170) REVERT: A 178 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8459 (mp) REVERT: B 138 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8432 (mtp85) REVERT: C 15 GLU cc_start: 0.7470 (mp0) cc_final: 0.7238 (mp0) REVERT: C 77 GLN cc_start: 0.4319 (OUTLIER) cc_final: 0.4024 (mt0) REVERT: C 131 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6828 (p90) REVERT: C 141 ASN cc_start: 0.6477 (m-40) cc_final: 0.6250 (m110) REVERT: C 259 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8087 (tptt) REVERT: D 50 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7420 (ttp80) REVERT: E 175 ARG cc_start: 0.8285 (tpp80) cc_final: 0.8074 (mmm-85) REVERT: F 61 ASP cc_start: 0.7226 (t70) cc_final: 0.6944 (t0) REVERT: F 91 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8596 (tp) REVERT: F 172 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7375 (ptm160) REVERT: G 156 GLU cc_start: 0.8501 (tt0) cc_final: 0.8295 (tt0) REVERT: G 176 PHE cc_start: 0.9138 (m-80) cc_final: 0.8866 (m-80) REVERT: G 300 GLN cc_start: 0.7854 (mp10) cc_final: 0.7573 (mp10) REVERT: H 89 ASP cc_start: 0.8431 (t70) cc_final: 0.7934 (t0) REVERT: H 293 LYS cc_start: 0.8102 (tttt) cc_final: 0.7682 (mtpt) REVERT: I 6 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6693 (mmm) REVERT: I 8 GLU cc_start: 0.7427 (pp20) cc_final: 0.6865 (pp20) REVERT: I 9 ILE cc_start: 0.8319 (mt) cc_final: 0.7495 (mt) REVERT: I 69 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7305 (mt-10) REVERT: I 120 ASN cc_start: 0.8033 (m110) cc_final: 0.7521 (m110) REVERT: J 6 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7697 (mmt) REVERT: J 73 LYS cc_start: 0.8252 (pttp) cc_final: 0.7840 (pttp) outliers start: 67 outliers final: 47 residues processed: 336 average time/residue: 0.1735 time to fit residues: 88.8956 Evaluate side-chains 350 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 38 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 189 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 261 optimal weight: 0.2980 chunk 312 optimal weight: 40.0000 chunk 64 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 219 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS B 114 HIS C 77 GLN E 127 ASN H 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.176528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.144721 restraints weight = 40168.186| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.04 r_work: 0.3077 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24730 Z= 0.206 Angle : 0.723 13.961 33691 Z= 0.341 Chirality : 0.054 0.539 3617 Planarity : 0.004 0.041 4314 Dihedral : 11.296 161.214 4105 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.42 % Allowed : 23.59 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.15), residues: 3092 helix: 0.87 (0.17), residues: 963 sheet: -0.43 (0.24), residues: 489 loop : -1.92 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 184 TYR 0.027 0.002 TYR J 89 PHE 0.016 0.002 PHE G 95 TRP 0.017 0.001 TRP A 263 HIS 0.009 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (24729) covalent geometry : angle 0.72285 / 0.34 (33691) hydrogen bonds : bond 0.03283 / 2.23 ( 902) hydrogen bonds : angle 4.45519 / 3.14 ( 2622) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 301 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5447 (tpp80) cc_final: 0.4665 (ttp-170) REVERT: A 178 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 252 SER cc_start: 0.8089 (t) cc_final: 0.7697 (p) REVERT: B 138 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8512 (mtp85) REVERT: B 200 LEU cc_start: 0.8269 (tp) cc_final: 0.7831 (tt) REVERT: B 313 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8422 (mp) REVERT: C 77 GLN cc_start: 0.4094 (OUTLIER) cc_final: 0.3735 (mt0) REVERT: C 131 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.6846 (p90) REVERT: C 259 LYS cc_start: 0.8353 (ttmm) cc_final: 0.8135 (tptt) REVERT: D 140 HIS cc_start: 0.8596 (m170) cc_final: 0.8231 (m170) REVERT: E 175 ARG cc_start: 0.8357 (tpp80) cc_final: 0.8146 (mmm-85) REVERT: F 91 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8659 (tp) REVERT: F 172 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7383 (ptm160) REVERT: G 300 GLN cc_start: 0.7834 (mp10) cc_final: 0.7555 (mp10) REVERT: H 89 ASP cc_start: 0.8436 (t70) cc_final: 0.7920 (t0) REVERT: I 6 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6745 (mmm) REVERT: I 8 GLU cc_start: 0.7562 (pp20) cc_final: 0.6986 (pp20) REVERT: I 9 ILE cc_start: 0.8324 (mt) cc_final: 0.7515 (mt) REVERT: J 6 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7756 (mmt) outliers start: 75 outliers final: 54 residues processed: 350 average time/residue: 0.1808 time to fit residues: 96.5589 Evaluate side-chains 345 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 301 LYS Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 307 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 259 optimal weight: 0.4980 chunk 114 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 284 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 114 HIS B 282 ASN C 77 GLN E 127 ASN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.179796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.142150 restraints weight = 45356.994| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 4.29 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24730 Z= 0.134 Angle : 0.669 13.131 33691 Z= 0.316 Chirality : 0.050 0.416 3617 Planarity : 0.004 0.084 4314 Dihedral : 11.199 159.194 4105 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.65 % Allowed : 24.68 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 3092 helix: 1.04 (0.18), residues: 957 sheet: -0.31 (0.25), residues: 460 loop : -1.87 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 184 TYR 0.022 0.001 TYR I 54 PHE 0.012 0.001 PHE G 95 TRP 0.012 0.001 TRP A 263 HIS 0.010 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (24729) covalent geometry : angle 0.66937 / 0.32 (33691) hydrogen bonds : bond 0.02937 / 2.00 ( 902) hydrogen bonds : angle 4.33701 / 3.07 ( 2622) Misc. bond : bond 0.00030 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 307 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5816 (tpp80) cc_final: 0.5454 (ttp-170) REVERT: A 178 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 252 SER cc_start: 0.7931 (t) cc_final: 0.7639 (p) REVERT: B 97 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.6932 (tt) REVERT: B 200 LEU cc_start: 0.8043 (tp) cc_final: 0.7653 (tt) REVERT: C 131 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6909 (p90) REVERT: D 50 ARG cc_start: 0.7444 (ttp80) cc_final: 0.7110 (ttp-170) REVERT: D 140 HIS cc_start: 0.8126 (m170) cc_final: 0.7691 (m170) REVERT: E 268 ASP cc_start: 0.8697 (p0) cc_final: 0.8288 (p0) REVERT: F 172 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7254 (ptm160) REVERT: F 314 ARG cc_start: 0.7558 (mpt-90) cc_final: 0.7317 (mpt-90) REVERT: H 89 ASP cc_start: 0.7978 (t70) cc_final: 0.7525 (t0) REVERT: I 8 GLU cc_start: 0.7124 (pp20) cc_final: 0.6538 (pp20) REVERT: I 9 ILE cc_start: 0.8088 (mt) cc_final: 0.7332 (mt) REVERT: I 120 ASN cc_start: 0.7948 (m110) cc_final: 0.7443 (m110) REVERT: J 6 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6864 (mmt) REVERT: J 122 ARG cc_start: 0.7578 (tmt-80) cc_final: 0.7288 (tmt-80) outliers start: 58 outliers final: 47 residues processed: 341 average time/residue: 0.1681 time to fit residues: 87.8121 Evaluate side-chains 347 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 301 LYS Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 166 optimal weight: 0.9980 chunk 235 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 223 optimal weight: 0.0070 chunk 189 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN J 120 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.183056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145681 restraints weight = 33710.160| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.14 r_work: 0.3078 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.250 24730 Z= 0.194 Angle : 0.872 59.175 33691 Z= 0.488 Chirality : 0.055 1.407 3617 Planarity : 0.004 0.129 4314 Dihedral : 11.204 159.184 4105 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.69 % Allowed : 24.73 % Favored : 72.58 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 3092 helix: 1.04 (0.18), residues: 957 sheet: -0.30 (0.25), residues: 460 loop : -1.86 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 161 TYR 0.020 0.001 TYR I 95 PHE 0.012 0.001 PHE G 95 TRP 0.051 0.001 TRP E 270 HIS 0.171 0.003 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (24729) covalent geometry : angle 0.87236 / 0.49 (33691) hydrogen bonds : bond 0.02945 / 2.01 ( 902) hydrogen bonds : angle 4.34034 / 3.07 ( 2622) Misc. bond : bond 0.00030 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5457.19 seconds wall clock time: 94 minutes 15.35 seconds (5655.35 seconds total)