Starting phenix.real_space_refine on Thu Mar 5 16:41:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ecv_31058/03_2026/7ecv_31058.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ecv_31058/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ecv_31058/03_2026/7ecv_31058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ecv_31058/03_2026/7ecv_31058.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ecv_31058/03_2026/7ecv_31058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ecv_31058/03_2026/7ecv_31058.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 13, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 22, 'rna3p': 37} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.41, per 1000 atoms: 0.27 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 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: 2.69 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: 3.99 Time building geometry restraints manager: 2.66 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: 32385 1.97 - 3.94: 1135 3.94 - 5.90: 127 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 - 32.37: 13809 32.37 - 64.74: 605 64.74 - 97.11: 74 97.11 - 129.49: 1 129.49 - 161.86: 4 Dihedral angle restraints: 14493 sinusoidal: 6113 harmonic: 8380 Sorted by residual: dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 47.63 152.37 1 1.50e+01 4.44e-03 8.05e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 56.99 143.01 1 1.50e+01 4.44e-03 7.67e+01 dihedral pdb=" O4' U M 35 " pdb=" C1' U M 35 " pdb=" N1 U M 35 " pdb=" C2 U M 35 " ideal model delta sinusoidal sigma weight residual -160.00 -78.28 -81.72 1 1.50e+01 4.44e-03 3.65e+01 ... (remaining 14490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3011 0.067 - 0.133: 526 0.133 - 0.200: 70 0.200 - 0.266: 9 0.266 - 0.333: 1 Chirality restraints: 3617 Sorted by residual: 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=" CB VAL L 42 " pdb=" CA VAL L 42 " pdb=" CG1 VAL L 42 " pdb=" CG2 VAL L 42 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.520 Find NCS groups from input model: 0.370 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.856 9.841 33691 Z= 0.482 Chirality : 0.052 0.333 3617 Planarity : 0.006 0.067 4314 Dihedral : 17.828 161.857 9297 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 covalent geometry : bond 0.00593 (24729) covalent geometry : angle 0.85560 (33691) hydrogen bonds : bond 0.14006 ( 902) hydrogen bonds : angle 6.93222 ( 2622) Misc. bond : bond 0.38794 ( 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 : 0.753 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: 0.1996 time to fit residues: 134.1785 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 : 0.768 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 64 HIS B 69 GLN B 82 ASN B 89 ASN B 104 HIS B 114 HIS B 172 ASN B 173 GLN C 77 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.177695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.138772 restraints weight = 34592.714| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.57 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24730 Z= 0.134 Angle : 0.569 11.067 33691 Z= 0.300 Chirality : 0.041 0.202 3617 Planarity : 0.004 0.056 4314 Dihedral : 15.212 177.496 4358 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.27 % Rotamer: Outliers : 3.19 % Allowed : 16.93 % Favored : 79.88 % 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: -2.75 (0.14), residues: 3092 helix: -0.86 (0.16), residues: 965 sheet: -1.32 (0.23), residues: 498 loop : -2.67 (0.13), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 175 TYR 0.016 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 covalent geometry : bond 0.00302 (24729) covalent geometry : angle 0.56868 (33691) hydrogen bonds : bond 0.03398 ( 902) hydrogen bonds : angle 4.89925 ( 2622) Misc. bond : bond 0.00037 ( 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 427 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 357 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 ASN cc_start: 0.8588 (m-40) cc_final: 0.8163 (m-40) REVERT: B 301 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8116 (pp) REVERT: C 25 MET cc_start: 0.7257 (mtm) cc_final: 0.6837 (mtm) REVERT: C 131 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7215 (p90) REVERT: C 283 GLU cc_start: 0.7593 (tp30) cc_final: 0.7272 (tp30) REVERT: E 264 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8622 (mt) REVERT: E 322 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7249 (mt0) REVERT: F 172 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7274 (ptm160) REVERT: G 19 ASP cc_start: 0.7577 (t0) cc_final: 0.7315 (t0) REVERT: G 89 ASP cc_start: 0.8483 (p0) cc_final: 0.8277 (p0) REVERT: H 75 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8846 (p0) REVERT: H 89 ASP cc_start: 0.7936 (t70) cc_final: 0.7513 (t0) REVERT: H 230 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7549 (mt-10) REVERT: I 8 GLU cc_start: 0.7062 (pp20) cc_final: 0.6553 (pp20) REVERT: I 9 ILE cc_start: 0.8215 (mt) cc_final: 0.7549 (mt) REVERT: I 120 ASN cc_start: 0.8232 (m110) cc_final: 0.7722 (m110) REVERT: J 81 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7352 (mm-30) outliers start: 70 outliers final: 42 residues processed: 404 average time/residue: 0.1864 time to fit residues: 112.2578 Evaluate side-chains 351 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 303 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 322 GLN 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 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: 4.9990 chunk 121 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 164 HIS C 329 ASN D 262 ASN E 127 ASN F 83 ASN F 329 ASN H 167 GLN H 329 ASN I 12 ASN I 21 HIS ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 GLN J 120 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.176567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.143164 restraints weight = 40056.037| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.41 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24730 Z= 0.232 Angle : 0.621 9.900 33691 Z= 0.325 Chirality : 0.043 0.200 3617 Planarity : 0.004 0.048 4314 Dihedral : 15.039 169.665 4344 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.86 % Favored : 92.11 % Rotamer: Outliers : 4.74 % Allowed : 18.61 % Favored : 76.64 % 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: -2.23 (0.14), residues: 3092 helix: -0.12 (0.17), residues: 951 sheet: -1.17 (0.24), residues: 489 loop : -2.50 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 189 TYR 0.019 0.002 TYR E 247 PHE 0.019 0.002 PHE G 95 TRP 0.014 0.001 TRP C 30 HIS 0.009 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00536 (24729) covalent geometry : angle 0.62054 (33691) hydrogen bonds : bond 0.03755 ( 902) hydrogen bonds : angle 4.83483 ( 2622) Misc. bond : bond 0.00113 ( 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 420 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 316 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8560 (mp) REVERT: B 301 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8016 (pp) REVERT: B 313 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8264 (mp) REVERT: C 25 MET cc_start: 0.7144 (mtm) cc_final: 0.6804 (mtm) REVERT: C 77 GLN cc_start: 0.4844 (OUTLIER) cc_final: 0.4171 (mp10) REVERT: C 131 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7141 (p90) REVERT: C 141 ASN cc_start: 0.7066 (m110) cc_final: 0.6733 (m110) REVERT: C 329 ASN cc_start: 0.8403 (t0) cc_final: 0.7486 (t0) REVERT: E 175 ARG cc_start: 0.7431 (ttm170) cc_final: 0.7173 (ttm170) REVERT: E 322 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7228 (mt0) REVERT: F 172 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7358 (ptm160) REVERT: F 291 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7735 (mm-40) REVERT: G 50 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8119 (ttt-90) REVERT: H 75 ASN cc_start: 0.9255 (OUTLIER) cc_final: 0.8932 (p0) REVERT: H 89 ASP cc_start: 0.8125 (t70) cc_final: 0.7671 (t0) REVERT: I 8 GLU cc_start: 0.7125 (pp20) cc_final: 0.6607 (pp20) REVERT: I 9 ILE cc_start: 0.8089 (mt) cc_final: 0.7456 (mt) REVERT: I 120 ASN cc_start: 0.8175 (m110) cc_final: 0.7605 (m110) REVERT: J 29 ASN cc_start: 0.5334 (m-40) cc_final: 0.5087 (m110) REVERT: J 122 ARG cc_start: 0.7561 (tmt-80) cc_final: 0.7329 (tmt-80) outliers start: 104 outliers final: 57 residues processed: 383 average time/residue: 0.1800 time to fit residues: 105.0023 Evaluate side-chains 357 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 4 THR 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 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 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 46 GLU 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 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 320 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 46 GLU 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 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 50 ARG 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 Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 80 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 57 optimal weight: 50.0000 chunk 107 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 308 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 95 optimal weight: 0.0070 chunk 171 optimal weight: 0.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 114 HIS B 172 ASN C 77 GLN E 127 ASN H 167 GLN H 329 ASN I 53 GLN ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.178784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.144631 restraints weight = 40396.927| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.59 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24730 Z= 0.100 Angle : 0.521 13.090 33691 Z= 0.273 Chirality : 0.039 0.200 3617 Planarity : 0.004 0.045 4314 Dihedral : 14.771 169.821 4342 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 3.47 % Allowed : 20.76 % Favored : 75.78 % 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: -1.72 (0.15), residues: 3092 helix: 0.47 (0.17), residues: 957 sheet: -0.93 (0.24), residues: 467 loop : -2.27 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 150 TYR 0.014 0.001 TYR I 95 PHE 0.014 0.001 PHE B 152 TRP 0.025 0.001 TRP C 30 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00221 (24729) covalent geometry : angle 0.52107 (33691) hydrogen bonds : bond 0.02891 ( 902) hydrogen bonds : angle 4.44183 ( 2622) Misc. bond : bond 0.00085 ( 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 425 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 349 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5745 (tpp80) cc_final: 0.5339 (ttp-170) REVERT: A 178 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 82 ASN cc_start: 0.8546 (m-40) cc_final: 0.8121 (m-40) REVERT: B 301 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8051 (pp) REVERT: C 25 MET cc_start: 0.7201 (mtm) cc_final: 0.6912 (mtm) REVERT: C 131 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7068 (p90) REVERT: F 37 GLN cc_start: 0.8234 (mm110) cc_final: 0.7777 (mm-40) REVERT: G 219 ILE cc_start: 0.8852 (mm) cc_final: 0.8631 (mt) REVERT: G 300 GLN cc_start: 0.7619 (mp10) cc_final: 0.7111 (mp10) REVERT: H 76 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8020 (mt) REVERT: H 89 ASP cc_start: 0.7848 (t70) cc_final: 0.7468 (t0) REVERT: H 91 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8847 (tp) REVERT: I 120 ASN cc_start: 0.8173 (m110) cc_final: 0.7841 (m110) REVERT: J 29 ASN cc_start: 0.5277 (m-40) cc_final: 0.5019 (m110) REVERT: J 76 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6420 (tttt) outliers start: 76 outliers final: 45 residues processed: 395 average time/residue: 0.1753 time to fit residues: 105.3069 Evaluate side-chains 355 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 304 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 186 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 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 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 320 VAL Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 76 LEU 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 288 VAL Chi-restraints excluded: chain H residue 301 LYS Chi-restraints excluded: chain H residue 329 ASN 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: 4.9990 chunk 55 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 chunk 233 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 51 optimal weight: 40.0000 chunk 120 optimal weight: 7.9990 chunk 309 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS C 77 GLN C 163 ASN E 127 ASN F 241 GLN H 167 GLN H 329 ASN J 120 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.171132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.141597 restraints weight = 40642.632| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.09 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24730 Z= 0.261 Angle : 0.641 15.817 33691 Z= 0.332 Chirality : 0.044 0.202 3617 Planarity : 0.004 0.043 4314 Dihedral : 14.933 168.488 4337 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.31 % Favored : 91.65 % Rotamer: Outliers : 4.65 % Allowed : 20.99 % Favored : 74.36 % 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: -1.70 (0.15), residues: 3092 helix: 0.49 (0.17), residues: 952 sheet: -0.91 (0.24), residues: 485 loop : -2.27 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 150 TYR 0.024 0.002 TYR E 247 PHE 0.020 0.002 PHE H 95 TRP 0.013 0.001 TRP C 30 HIS 0.011 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00608 (24729) covalent geometry : angle 0.64072 (33691) hydrogen bonds : bond 0.03671 ( 902) hydrogen bonds : angle 4.70834 ( 2622) Misc. bond : bond 0.00019 ( 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 394 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 292 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5631 (tpp80) cc_final: 0.5410 (ttp-170) REVERT: A 178 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8481 (mp) REVERT: B 301 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8094 (pp) REVERT: B 313 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8280 (mp) REVERT: C 131 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7064 (p90) REVERT: F 91 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8422 (tp) REVERT: F 172 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7236 (ptm160) REVERT: G 50 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8156 (ttt-90) REVERT: H 75 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8932 (p0) REVERT: H 89 ASP cc_start: 0.8240 (t70) cc_final: 0.7777 (t0) REVERT: H 91 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8659 (tp) REVERT: I 120 ASN cc_start: 0.8173 (m110) cc_final: 0.7636 (m110) outliers start: 102 outliers final: 64 residues processed: 368 average time/residue: 0.1801 time to fit residues: 100.1620 Evaluate side-chains 360 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 287 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 126 ILE 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 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 186 PHE 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 D residue 18 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 97 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 277 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 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 7 SER Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR 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 50 ARG Chi-restraints excluded: chain G residue 99 VAL 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 G residue 288 VAL 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 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 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 H residue 329 ASN Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 98 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 303 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 50.0000 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 108 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 114 HIS D 141 ASN E 127 ASN F 229 GLN H 167 GLN H 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.182576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.144078 restraints weight = 39834.876| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 4.02 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24730 Z= 0.109 Angle : 0.528 13.532 33691 Z= 0.276 Chirality : 0.039 0.199 3617 Planarity : 0.004 0.043 4314 Dihedral : 14.690 169.680 4337 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.56 % Allowed : 22.35 % Favored : 74.09 % 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: -1.32 (0.15), residues: 3092 helix: 0.86 (0.18), residues: 945 sheet: -0.71 (0.24), residues: 474 loop : -2.05 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 10 TYR 0.014 0.001 TYR I 95 PHE 0.014 0.001 PHE B 152 TRP 0.012 0.001 TRP B 316 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00244 (24729) covalent geometry : angle 0.52795 (33691) hydrogen bonds : bond 0.02907 ( 902) hydrogen bonds : angle 4.37151 ( 2622) Misc. bond : bond 0.00045 ( 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 395 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 317 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5740 (tpp80) cc_final: 0.5288 (ttp-170) REVERT: A 178 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8370 (mp) REVERT: B 301 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8047 (pp) REVERT: C 131 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.6977 (p90) REVERT: C 283 GLU cc_start: 0.7587 (tp30) cc_final: 0.7304 (tp30) REVERT: D 305 TYR cc_start: 0.8909 (m-80) cc_final: 0.8632 (m-80) REVERT: F 172 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7166 (ptm160) REVERT: G 219 ILE cc_start: 0.8848 (mm) cc_final: 0.8604 (mt) REVERT: G 300 GLN cc_start: 0.7631 (mp10) cc_final: 0.7162 (mp10) REVERT: H 76 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8001 (mt) REVERT: H 89 ASP cc_start: 0.8155 (t70) cc_final: 0.7690 (t0) REVERT: H 91 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8863 (tp) REVERT: I 120 ASN cc_start: 0.8125 (m110) cc_final: 0.7710 (m110) REVERT: J 6 MET cc_start: 0.7434 (mmt) cc_final: 0.7124 (mmt) outliers start: 78 outliers final: 51 residues processed: 368 average time/residue: 0.1783 time to fit residues: 99.9040 Evaluate side-chains 345 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 288 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 301 LEU 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 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 C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 46 GLU 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 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 320 VAL Chi-restraints excluded: chain E residue 321 GLU 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 213 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 76 LEU 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 288 VAL Chi-restraints excluded: chain H residue 301 LYS Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 38 VAL 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: 0.9980 chunk 147 optimal weight: 0.0050 chunk 300 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 228 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 266 optimal weight: 0.9980 chunk 272 optimal weight: 0.5980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 114 HIS E 127 ASN H 167 GLN ** H 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.178664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.137961 restraints weight = 32386.155| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.47 r_work: 0.3121 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2717 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= 0.097 Angle : 0.520 15.420 33691 Z= 0.269 Chirality : 0.039 0.208 3617 Planarity : 0.003 0.043 4314 Dihedral : 14.558 168.746 4337 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.24 % Allowed : 23.27 % Favored : 73.49 % 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: -1.15 (0.15), residues: 3092 helix: 0.97 (0.18), residues: 964 sheet: -0.42 (0.25), residues: 449 loop : -2.01 (0.14), residues: 1679 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 0.032 0.001 PHE C 304 TRP 0.013 0.001 TRP C 30 HIS 0.003 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00217 (24729) covalent geometry : angle 0.51983 (33691) hydrogen bonds : bond 0.02740 ( 902) hydrogen bonds : angle 4.22479 ( 2622) Misc. bond : bond 0.00038 ( 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 399 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 328 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5471 (tpp80) cc_final: 0.4677 (ttp-170) REVERT: A 178 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8529 (mp) REVERT: C 30 TRP cc_start: 0.5253 (m100) cc_final: 0.4926 (m100) REVERT: C 131 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6853 (p90) REVERT: C 218 ARG cc_start: 0.6663 (mtm110) cc_final: 0.6173 (tpt90) REVERT: E 302 LEU cc_start: 0.8761 (mt) cc_final: 0.8463 (mp) REVERT: F 61 ASP cc_start: 0.7184 (t70) cc_final: 0.6922 (t0) REVERT: F 172 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7367 (ptm160) REVERT: F 237 ASP cc_start: 0.7208 (t0) cc_final: 0.6826 (t0) REVERT: G 300 GLN cc_start: 0.7817 (mp10) cc_final: 0.7382 (mp10) REVERT: H 76 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8344 (mt) REVERT: H 89 ASP cc_start: 0.8371 (t70) cc_final: 0.7917 (t0) REVERT: H 91 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8836 (tp) REVERT: I 120 ASN cc_start: 0.8193 (m110) cc_final: 0.7708 (m110) REVERT: J 6 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7705 (mmt) REVERT: J 73 LYS cc_start: 0.7723 (ptpp) cc_final: 0.7383 (pttm) REVERT: J 119 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7817 (tm-30) outliers start: 71 outliers final: 43 residues processed: 377 average time/residue: 0.1730 time to fit residues: 99.4568 Evaluate side-chains 356 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 307 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 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 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 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 320 VAL Chi-restraints excluded: chain E residue 321 GLU 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 213 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 76 LEU 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 288 VAL Chi-restraints excluded: chain H residue 301 LYS Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 77 SER 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: 2.9990 chunk 111 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 218 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN C 77 GLN E 127 ASN E 291 GLN H 167 GLN ** H 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 ASN J 29 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.183385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.142942 restraints weight = 39860.943| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 4.24 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24730 Z= 0.118 Angle : 0.533 16.234 33691 Z= 0.274 Chirality : 0.040 0.284 3617 Planarity : 0.004 0.042 4314 Dihedral : 14.536 168.377 4337 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.38 % Allowed : 23.95 % 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: -1.05 (0.15), residues: 3092 helix: 1.09 (0.18), residues: 956 sheet: -0.38 (0.25), residues: 450 loop : -1.94 (0.14), residues: 1686 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 0.026 0.001 PHE C 304 TRP 0.011 0.001 TRP C 30 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00270 (24729) covalent geometry : angle 0.53282 (33691) hydrogen bonds : bond 0.02810 ( 902) hydrogen bonds : angle 4.23550 ( 2622) Misc. bond : bond 0.00028 ( 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 388 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 314 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.2054 (ttt) cc_final: 0.1726 (ttm) REVERT: L 10 ARG cc_start: 0.5861 (tpp80) cc_final: 0.5343 (ttp-170) REVERT: A 178 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8359 (mp) REVERT: C 15 GLU cc_start: 0.7174 (mp0) cc_final: 0.6969 (mp0) REVERT: C 30 TRP cc_start: 0.5488 (m100) cc_final: 0.5182 (m100) REVERT: C 77 GLN cc_start: 0.4551 (OUTLIER) cc_final: 0.4290 (mt0) REVERT: C 131 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6938 (p90) REVERT: C 141 ASN cc_start: 0.5905 (m-40) cc_final: 0.5440 (m110) REVERT: C 218 ARG cc_start: 0.6136 (mtm110) cc_final: 0.5857 (tpt90) REVERT: F 37 GLN cc_start: 0.8345 (mm110) cc_final: 0.8077 (mm110) REVERT: F 172 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7214 (ptm160) REVERT: F 237 ASP cc_start: 0.6969 (t0) cc_final: 0.6680 (t0) REVERT: G 136 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7222 (ttp80) REVERT: G 300 GLN cc_start: 0.7598 (mp10) cc_final: 0.7234 (mp10) REVERT: H 89 ASP cc_start: 0.7863 (t70) cc_final: 0.7486 (t0) REVERT: H 91 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8694 (tp) REVERT: I 120 ASN cc_start: 0.8098 (m110) cc_final: 0.7671 (m110) REVERT: J 6 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7045 (mmt) REVERT: J 119 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7401 (tm-30) outliers start: 74 outliers final: 48 residues processed: 363 average time/residue: 0.1715 time to fit residues: 95.0598 Evaluate side-chains 354 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 299 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 305 HIS Chi-restraints excluded: chain B residue 306 HIS 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 260 ILE 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 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 320 VAL Chi-restraints excluded: chain E residue 321 GLU 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 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 15 GLU 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 329 ASN Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 77 SER 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: 3.9990 chunk 95 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 261 optimal weight: 0.0870 chunk 312 optimal weight: 40.0000 chunk 64 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 235 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN E 127 ASN H 167 GLN ** H 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.178845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.146601 restraints weight = 39774.540| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.14 r_work: 0.3073 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24730 Z= 0.172 Angle : 0.577 16.986 33691 Z= 0.298 Chirality : 0.041 0.231 3617 Planarity : 0.004 0.041 4314 Dihedral : 14.589 167.788 4337 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.10 % Allowed : 24.27 % Favored : 72.63 % 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: 0.97 (0.18), residues: 963 sheet: -0.43 (0.25), residues: 465 loop : -1.97 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 184 TYR 0.020 0.002 TYR I 95 PHE 0.026 0.002 PHE C 304 TRP 0.013 0.001 TRP A 263 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00398 (24729) covalent geometry : angle 0.57713 (33691) hydrogen bonds : bond 0.03124 ( 902) hydrogen bonds : angle 4.36869 ( 2622) Misc. bond : bond 0.00018 ( 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 368 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 300 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.1895 (ttt) cc_final: 0.1530 (ttm) REVERT: L 10 ARG cc_start: 0.5464 (tpp80) cc_final: 0.4727 (ttp-170) REVERT: A 178 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8685 (mp) REVERT: B 200 LEU cc_start: 0.8332 (tp) cc_final: 0.7895 (tt) REVERT: C 15 GLU cc_start: 0.7515 (mp0) cc_final: 0.7239 (mp0) REVERT: C 30 TRP cc_start: 0.5454 (m100) cc_final: 0.4995 (m100) REVERT: C 131 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6890 (p90) REVERT: C 141 ASN cc_start: 0.6223 (m-40) cc_final: 0.5641 (m110) REVERT: F 172 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7463 (ptm160) REVERT: F 237 ASP cc_start: 0.7175 (t0) cc_final: 0.6746 (t0) REVERT: G 45 ARG cc_start: 0.8216 (mtm110) cc_final: 0.7697 (mtm110) REVERT: G 300 GLN cc_start: 0.7860 (mp10) cc_final: 0.7418 (mp10) REVERT: H 89 ASP cc_start: 0.8498 (t70) cc_final: 0.7995 (t0) REVERT: I 120 ASN cc_start: 0.8052 (m110) cc_final: 0.7500 (m110) REVERT: J 6 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7694 (mmt) REVERT: J 81 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8407 (mm-30) REVERT: J 119 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7797 (tm-30) REVERT: J 122 ARG cc_start: 0.7928 (tmt-80) cc_final: 0.7363 (tmt-80) outliers start: 68 outliers final: 50 residues processed: 345 average time/residue: 0.1794 time to fit residues: 93.4956 Evaluate side-chains 345 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 291 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 89 ASP 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 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 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 321 GLU Chi-restraints excluded: chain F residue 15 GLU 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 219 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 15 GLU 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 I residue 12 ASN 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: 5.9990 chunk 136 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 259 optimal weight: 0.4980 chunk 114 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS E 127 ASN H 167 GLN H 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.178130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.147821 restraints weight = 44982.920| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.43 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24730 Z= 0.138 Angle : 0.559 17.116 33691 Z= 0.288 Chirality : 0.040 0.243 3617 Planarity : 0.004 0.042 4314 Dihedral : 14.534 167.732 4337 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.83 % Allowed : 24.73 % Favored : 72.45 % 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: 1.05 (0.18), residues: 963 sheet: -0.33 (0.25), residues: 448 loop : -1.93 (0.14), residues: 1681 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 0.030 0.001 PHE C 304 TRP 0.012 0.001 TRP A 263 HIS 0.007 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00318 (24729) covalent geometry : angle 0.55893 (33691) hydrogen bonds : bond 0.02958 ( 902) hydrogen bonds : angle 4.32045 ( 2622) Misc. bond : bond 0.00036 ( 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 361 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 299 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.2406 (ttt) cc_final: 0.2054 (ttm) REVERT: L 10 ARG cc_start: 0.5856 (tpp80) cc_final: 0.5647 (ttp-170) REVERT: A 178 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8394 (mp) REVERT: B 200 LEU cc_start: 0.7975 (tp) cc_final: 0.7605 (tt) REVERT: B 313 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8230 (mp) REVERT: C 131 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6907 (p90) REVERT: C 141 ASN cc_start: 0.5646 (m-40) cc_final: 0.5303 (m110) REVERT: E 50 ARG cc_start: 0.7975 (ptt180) cc_final: 0.7538 (tmm-80) REVERT: F 37 GLN cc_start: 0.8372 (mm110) cc_final: 0.8122 (mm-40) REVERT: F 172 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7272 (ptm160) REVERT: F 237 ASP cc_start: 0.6783 (t0) cc_final: 0.6563 (t0) REVERT: F 314 ARG cc_start: 0.7500 (mpt-90) cc_final: 0.7242 (mpt-90) REVERT: G 45 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7438 (mtm110) REVERT: G 300 GLN cc_start: 0.7473 (mp10) cc_final: 0.7098 (mp10) REVERT: H 89 ASP cc_start: 0.8054 (t70) cc_final: 0.7614 (t0) REVERT: I 120 ASN cc_start: 0.8062 (m110) cc_final: 0.7586 (m110) REVERT: J 6 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6674 (mmt) REVERT: J 81 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7592 (mm-30) REVERT: J 122 ARG cc_start: 0.7551 (tmt-80) cc_final: 0.7009 (tmt-80) outliers start: 62 outliers final: 52 residues processed: 337 average time/residue: 0.1803 time to fit residues: 91.0260 Evaluate side-chains 350 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 293 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 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 89 ASP 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 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 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 321 GLU Chi-restraints excluded: chain F residue 15 GLU 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 24 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR 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 280 ILE Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 12 ASN 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: 0.4980 chunk 235 optimal weight: 0.0980 chunk 307 optimal weight: 0.2980 chunk 144 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 263 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS E 127 ASN H 167 GLN H 322 GLN H 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.185142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.144859 restraints weight = 33396.025| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.96 r_work: 0.3050 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24730 Z= 0.126 Angle : 0.694 59.183 33691 Z= 0.388 Chirality : 0.043 1.061 3617 Planarity : 0.004 0.041 4314 Dihedral : 14.536 167.735 4337 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.74 % Allowed : 24.86 % Favored : 72.40 % Cbeta Deviations : 0.04 % 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: -1.02 (0.15), residues: 3092 helix: 1.08 (0.18), residues: 963 sheet: -0.32 (0.25), residues: 448 loop : -1.92 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 184 TYR 0.019 0.001 TYR I 95 PHE 0.026 0.001 PHE C 304 TRP 0.030 0.001 TRP C 30 HIS 0.009 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00279 (24729) covalent geometry : angle 0.69376 (33691) hydrogen bonds : bond 0.02945 ( 902) hydrogen bonds : angle 4.32124 ( 2622) Misc. bond : bond 0.00034 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4747.35 seconds wall clock time: 82 minutes 8.81 seconds (4928.81 seconds total)