Starting phenix.real_space_refine on Thu Mar 5 17:29:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e2d_30955/03_2026/7e2d_30955.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e2d_30955/03_2026/7e2d_30955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e2d_30955/03_2026/7e2d_30955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e2d_30955/03_2026/7e2d_30955.map" model { file = "/net/cci-nas-00/data/ceres_data/7e2d_30955/03_2026/7e2d_30955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e2d_30955/03_2026/7e2d_30955.cif" } resolution = 3.71 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1092 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 14797 2.51 5 N 4041 2.21 5 O 4406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 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: 23331 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1160 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "C" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1482 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "B" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1630 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1235 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1341 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 159} Chain breaks: 3 Chain: "F" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1470 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "G" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1648 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain breaks: 1 Chain: "H" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1180 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 138} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 4204 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 650} Link IDs: {'PTRANS': 16, 'TRANS': 771} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 2335 Unresolved non-hydrogen angles: 2973 Unresolved non-hydrogen dihedrals: 1927 Unresolved non-hydrogen chiralities: 228 Planarities with less than four sites: {'GLN:plan1': 30, 'PHE:plan': 42, 'GLU:plan': 61, 'ASP:plan': 38, 'HIS:plan': 9, 'TYR:plan': 22, 'ARG:plan': 24, 'ASN:plan1': 41, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 1235 Chain: "J" Number of atoms: 6332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6332 Classifications: {'peptide': 872} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 37, 'TRANS': 834} Chain breaks: 5 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 858 Unresolved non-hydrogen angles: 1097 Unresolved non-hydrogen dihedrals: 712 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'ASN:plan1': 16, 'ARG:plan': 10, 'GLN:plan1': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'ASP:plan': 18, 'TRP:plan': 3, 'GLU:plan': 11, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 419 Chain: "K" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1649 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'ASN:plan1': 6, 'ARG:plan': 4, 'GLU:plan': 7, 'HIS:plan': 4, 'ASP:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 5, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 185 Time building chain proxies: 4.56, per 1000 atoms: 0.20 Number of scatterers: 23331 At special positions: 0 Unit cell: (190.925, 261.84, 130.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 4406 8.00 N 4041 7.00 C 14797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 977.5 milliseconds 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6336 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 32 sheets defined 36.0% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 removed outlier: 4.223A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 120 removed outlier: 3.996A pdb=" N ALA A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.979A pdb=" N TYR C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 75 removed outlier: 5.017A pdb=" N GLU C 69 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 100 removed outlier: 4.038A pdb=" N SER C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS C 96 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 removed outlier: 3.824A pdb=" N CYS C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 removed outlier: 3.577A pdb=" N VAL C 155 " --> pdb=" O LEU C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 155' Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 112 through 139 removed outlier: 4.145A pdb=" N ARG B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 152 through 170 removed outlier: 4.097A pdb=" N ILE B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.895A pdb=" N LYS B 209 " --> pdb=" O ASN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'D' and resid 40 through 58 Processing helix chain 'D' and resid 99 through 110 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'E' and resid 31 through 50 removed outlier: 3.975A pdb=" N ILE E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA E 45 " --> pdb=" O HIS E 41 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 190 Processing helix chain 'E' and resid 204 through 219 removed outlier: 4.045A pdb=" N ASP E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU E 209 " --> pdb=" O ASN E 205 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 removed outlier: 5.073A pdb=" N GLU F 15 " --> pdb=" O LYS F 11 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 45 removed outlier: 3.580A pdb=" N TYR F 45 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 75 removed outlier: 4.078A pdb=" N VAL F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 93 through 98 removed outlier: 3.712A pdb=" N PHE F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 155 removed outlier: 3.750A pdb=" N GLY F 146 " --> pdb=" O ASN F 142 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 76 Processing helix chain 'G' and resid 79 through 107 removed outlier: 3.642A pdb=" N PHE G 83 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE G 94 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU G 100 " --> pdb=" O ILE G 96 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 192 removed outlier: 4.069A pdb=" N ILE G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU G 180 " --> pdb=" O ILE G 176 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN G 181 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TRP G 188 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER G 189 " --> pdb=" O GLY G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 229 No H-bonds generated for 'chain 'G' and resid 227 through 229' Processing helix chain 'G' and resid 230 through 242 removed outlier: 4.164A pdb=" N CYS G 234 " --> pdb=" O GLU G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 245 No H-bonds generated for 'chain 'G' and resid 243 through 245' Processing helix chain 'G' and resid 271 through 281 removed outlier: 3.931A pdb=" N LEU G 275 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG G 277 " --> pdb=" O GLN G 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 52 removed outlier: 4.213A pdb=" N GLU H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) Proline residue: H 38 - end of helix removed outlier: 3.572A pdb=" N LEU H 41 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP H 46 " --> pdb=" O HIS H 42 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 127 Processing helix chain 'H' and resid 129 through 146 Processing helix chain 'H' and resid 158 through 172 removed outlier: 3.609A pdb=" N ASP H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 269 Processing helix chain 'I' and resid 276 through 292 removed outlier: 3.703A pdb=" N TYR I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 317 removed outlier: 3.725A pdb=" N PHE I 309 " --> pdb=" O LEU I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 339 removed outlier: 4.003A pdb=" N SER I 336 " --> pdb=" O THR I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 369 removed outlier: 3.590A pdb=" N GLU I 350 " --> pdb=" O PRO I 346 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE I 351 " --> pdb=" O LEU I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 420 removed outlier: 4.010A pdb=" N GLU I 404 " --> pdb=" O THR I 400 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN I 405 " --> pdb=" O VAL I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 424 through 441 removed outlier: 3.635A pdb=" N VAL I 428 " --> pdb=" O ARG I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 452 Processing helix chain 'I' and resid 452 through 459 Processing helix chain 'I' and resid 466 through 481 removed outlier: 3.686A pdb=" N GLN I 473 " --> pdb=" O LEU I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 509 removed outlier: 3.898A pdb=" N PHE I 505 " --> pdb=" O LEU I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 514 No H-bonds generated for 'chain 'I' and resid 512 through 514' Processing helix chain 'I' and resid 515 through 529 removed outlier: 3.865A pdb=" N GLU I 519 " --> pdb=" O ASN I 515 " (cutoff:3.500A) Processing helix chain 'I' and resid 628 through 632 removed outlier: 4.145A pdb=" N GLY I 631 " --> pdb=" O ILE I 628 " (cutoff:3.500A) Processing helix chain 'I' and resid 862 through 875 removed outlier: 3.973A pdb=" N LEU I 875 " --> pdb=" O THR I 871 " (cutoff:3.500A) Processing helix chain 'I' and resid 880 through 885 removed outlier: 4.061A pdb=" N ILE I 884 " --> pdb=" O VAL I 880 " (cutoff:3.500A) Processing helix chain 'I' and resid 889 through 898 Processing helix chain 'I' and resid 921 through 930 removed outlier: 4.206A pdb=" N LYS I 925 " --> pdb=" O ILE I 921 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE I 930 " --> pdb=" O THR I 926 " (cutoff:3.500A) Processing helix chain 'I' and resid 933 through 938 Processing helix chain 'I' and resid 938 through 948 removed outlier: 3.896A pdb=" N LEU I 944 " --> pdb=" O LEU I 940 " (cutoff:3.500A) Processing helix chain 'I' and resid 957 through 962 Processing helix chain 'J' and resid 266 through 288 removed outlier: 3.523A pdb=" N ARG J 288 " --> pdb=" O LEU J 284 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 293 removed outlier: 3.787A pdb=" N ALA J 292 " --> pdb=" O TYR J 289 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU J 293 " --> pdb=" O VAL J 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 289 through 293' Processing helix chain 'J' and resid 307 through 327 Processing helix chain 'J' and resid 380 through 397 removed outlier: 4.264A pdb=" N ALA J 384 " --> pdb=" O ILE J 380 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET J 385 " --> pdb=" O SER J 381 " (cutoff:3.500A) Proline residue: J 388 - end of helix Processing helix chain 'J' and resid 402 through 417 Proline residue: J 410 - end of helix Processing helix chain 'J' and resid 426 through 442 Proline residue: J 436 - end of helix removed outlier: 4.117A pdb=" N VAL J 439 " --> pdb=" O ALA J 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 476 removed outlier: 4.530A pdb=" N LEU J 465 " --> pdb=" O SER J 461 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN J 467 " --> pdb=" O ASP J 463 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU J 476 " --> pdb=" O GLN J 472 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 495 removed outlier: 3.781A pdb=" N TYR J 491 " --> pdb=" O ARG J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 506 through 525 Processing helix chain 'J' and resid 526 through 543 Processing helix chain 'J' and resid 551 through 565 removed outlier: 3.714A pdb=" N ARG J 555 " --> pdb=" O HIS J 551 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU J 565 " --> pdb=" O ILE J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 585 through 602 removed outlier: 3.988A pdb=" N LEU J 594 " --> pdb=" O LYS J 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS J 597 " --> pdb=" O GLN J 593 " (cutoff:3.500A) Processing helix chain 'J' and resid 604 through 616 removed outlier: 3.744A pdb=" N VAL J 608 " --> pdb=" O ASP J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 617 through 619 No H-bonds generated for 'chain 'J' and resid 617 through 619' Processing helix chain 'J' and resid 627 through 635 removed outlier: 3.855A pdb=" N LEU J 631 " --> pdb=" O GLU J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 636 through 641 Processing helix chain 'J' and resid 897 through 909 Proline residue: J 903 - end of helix Processing helix chain 'J' and resid 1016 through 1028 removed outlier: 3.811A pdb=" N GLU J1020 " --> pdb=" O VAL J1016 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR J1021 " --> pdb=" O ASP J1017 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA J1028 " --> pdb=" O SER J1024 " (cutoff:3.500A) Processing helix chain 'J' and resid 1110 through 1129 removed outlier: 3.648A pdb=" N THR J1114 " --> pdb=" O ASN J1110 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG J1124 " --> pdb=" O LYS J1120 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER J1129 " --> pdb=" O GLU J1125 " (cutoff:3.500A) Processing helix chain 'J' and resid 1157 through 1165 removed outlier: 3.519A pdb=" N VAL J1161 " --> pdb=" O ASP J1157 " (cutoff:3.500A) Processing helix chain 'J' and resid 1166 through 1169 Processing helix chain 'K' and resid 237 through 249 removed outlier: 4.080A pdb=" N PHE K 247 " --> pdb=" O LEU K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 483 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.725A pdb=" N LEU A 19 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 7 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 84 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AA3, first strand: chain 'C' and resid 104 through 106 removed outlier: 3.717A pdb=" N PHE C 115 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 178 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 176 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 160 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.660A pdb=" N VAL B 96 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 175 through 178 removed outlier: 3.640A pdb=" N ASN B 175 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 184 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 262 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B 260 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 17 through 20 removed outlier: 3.761A pdb=" N PHE D 17 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER D 5 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 91 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP D 7 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 89 " --> pdb=" O TRP D 7 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ARG D 68 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE D 67 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR E 124 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER D 69 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU E 122 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER D 71 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG E 120 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 24 through 26 Processing sheet with id=AA8, first strand: chain 'F' and resid 104 through 106 removed outlier: 3.558A pdb=" N ASN F 104 " --> pdb=" O ILE F 118 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR F 174 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU F 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL F 164 " --> pdb=" O GLU F 175 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP F 162 " --> pdb=" O LYS F 177 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS F 179 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP F 158 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 34 through 36 removed outlier: 3.644A pdb=" N THR H 21 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR H 16 " --> pdb=" O ILE H 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 198 through 201 removed outlier: 3.690A pdb=" N TYR G 209 " --> pdb=" O ILE G 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 88 through 94 removed outlier: 5.389A pdb=" N GLY H 90 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA H 102 " --> pdb=" O GLY H 90 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE H 100 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 562 through 565 Processing sheet with id=AB4, first strand: chain 'I' and resid 593 through 594 removed outlier: 4.009A pdb=" N VAL I 593 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE I 609 " --> pdb=" O VAL I 593 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 674 through 675 removed outlier: 3.542A pdb=" N GLU I 728 " --> pdb=" O VAL I 689 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 722 through 723 Processing sheet with id=AB7, first strand: chain 'I' and resid 769 through 777 Processing sheet with id=AB8, first strand: chain 'I' and resid 819 through 820 removed outlier: 3.610A pdb=" N TYR I 819 " --> pdb=" O SER I 802 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU I 799 " --> pdb=" O ASN I 860 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN I 860 " --> pdb=" O LEU I 799 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER I 801 " --> pdb=" O ARG I 858 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN I 854 " --> pdb=" O SER I 805 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 988 through 992 removed outlier: 3.700A pdb=" N ASP I1031 " --> pdb=" O GLN I 992 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 1014 through 1016 removed outlier: 6.812A pdb=" N THR I1014 " --> pdb=" O GLU I1062 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU I1062 " --> pdb=" O THR I1014 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 772 through 773 removed outlier: 4.634A pdb=" N ASP J 751 " --> pdb=" O VAL J 773 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER J 755 " --> pdb=" O SER J 804 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER J 804 " --> pdb=" O SER J 755 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 860 through 861 Processing sheet with id=AC4, first strand: chain 'J' and resid 929 through 930 removed outlier: 6.805A pdb=" N ARG J 930 " --> pdb=" O MET J 970 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 1000 through 1004 removed outlier: 3.861A pdb=" N LEU J1042 " --> pdb=" O ILE J1076 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE J1044 " --> pdb=" O SER J1074 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 1134 through 1135 Processing sheet with id=AC7, first strand: chain 'J' and resid 1171 through 1177 removed outlier: 3.750A pdb=" N GLN J1174 " --> pdb=" O ILE J1193 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 1181 through 1182 removed outlier: 3.703A pdb=" N TYR J1261 " --> pdb=" O LEU J1286 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU J1262 " --> pdb=" O PHE J1216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE J1216 " --> pdb=" O GLU J1262 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER J1264 " --> pdb=" O VAL J1214 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL J1214 " --> pdb=" O SER J1264 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 215 through 223 removed outlier: 3.732A pdb=" N LYS K 223 " --> pdb=" O CYS K 227 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS K 227 " --> pdb=" O LYS K 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 284 through 285 removed outlier: 3.872A pdb=" N VAL K 285 " --> pdb=" O LYS K 258 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS K 258 " --> pdb=" O VAL K 285 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 306 through 311 Processing sheet with id=AD3, first strand: chain 'K' and resid 403 through 404 removed outlier: 3.645A pdb=" N PHE K 427 " --> pdb=" O PHE K 524 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE K 524 " --> pdb=" O PHE K 427 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA K 520 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 419 through 421 removed outlier: 6.114A pdb=" N LYS K 420 " --> pdb=" O VAL K 557 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER K 556 " --> pdb=" O TYR K 532 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 507 through 508 removed outlier: 3.836A pdb=" N GLU K 547 " --> pdb=" O ASP K 542 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2739 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6724 1.34 - 1.46: 5271 1.46 - 1.58: 11558 1.58 - 1.71: 1 1.71 - 1.83: 138 Bond restraints: 23692 Sorted by residual: bond pdb=" C GLY J 769 " pdb=" N PRO J 770 " ideal model delta sigma weight residual 1.334 1.377 -0.044 8.40e-03 1.42e+04 2.73e+01 bond pdb=" N GLN E 56 " pdb=" CA GLN E 56 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.15e+01 bond pdb=" CA ARG F 169 " pdb=" C ARG F 169 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.56e-02 4.11e+03 1.32e+01 bond pdb=" N MET J 909 " pdb=" CA MET J 909 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.69e+00 bond pdb=" N ILE J1215 " pdb=" CA ILE J1215 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.19e-02 7.06e+03 9.41e+00 ... (remaining 23687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.74: 31695 4.74 - 9.48: 482 9.48 - 14.22: 46 14.22 - 18.96: 11 18.96 - 23.71: 1 Bond angle restraints: 32235 Sorted by residual: angle pdb=" N VAL F 155 " pdb=" CA VAL F 155 " pdb=" C VAL F 155 " ideal model delta sigma weight residual 112.17 103.15 9.02 9.50e-01 1.11e+00 9.02e+01 angle pdb=" N PRO I 639 " pdb=" CA PRO I 639 " pdb=" CB PRO I 639 " ideal model delta sigma weight residual 103.25 112.01 -8.76 1.05e+00 9.07e-01 6.95e+01 angle pdb=" N PRO I 346 " pdb=" CA PRO I 346 " pdb=" CB PRO I 346 " ideal model delta sigma weight residual 103.25 111.92 -8.67 1.05e+00 9.07e-01 6.82e+01 angle pdb=" N PRO I 483 " pdb=" CA PRO I 483 " pdb=" CB PRO I 483 " ideal model delta sigma weight residual 103.25 111.89 -8.64 1.05e+00 9.07e-01 6.77e+01 angle pdb=" N PRO K 310 " pdb=" CA PRO K 310 " pdb=" CB PRO K 310 " ideal model delta sigma weight residual 103.25 111.70 -8.45 1.05e+00 9.07e-01 6.47e+01 ... (remaining 32230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 13011 18.12 - 36.24: 1026 36.24 - 54.35: 148 54.35 - 72.47: 42 72.47 - 90.59: 18 Dihedral angle restraints: 14245 sinusoidal: 4550 harmonic: 9695 Sorted by residual: dihedral pdb=" CA TYR J 648 " pdb=" C TYR J 648 " pdb=" N TRP J 649 " pdb=" CA TRP J 649 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR I 995 " pdb=" C THR I 995 " pdb=" N SER I 996 " pdb=" CA SER I 996 " ideal model delta harmonic sigma weight residual 180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR K 545 " pdb=" C THR K 545 " pdb=" N ASN K 546 " pdb=" CA ASN K 546 " ideal model delta harmonic sigma weight residual -180.00 -152.42 -27.58 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 14242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3261 0.099 - 0.198: 467 0.198 - 0.297: 85 0.297 - 0.396: 19 0.396 - 0.495: 4 Chirality restraints: 3836 Sorted by residual: chirality pdb=" CB THR G 219 " pdb=" CA THR G 219 " pdb=" OG1 THR G 219 " pdb=" CG2 THR G 219 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CB ILE J 760 " pdb=" CA ILE J 760 " pdb=" CG1 ILE J 760 " pdb=" CG2 ILE J 760 " both_signs ideal model delta sigma weight residual False 2.64 3.09 -0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CB ILE F 143 " pdb=" CA ILE F 143 " pdb=" CG1 ILE F 143 " pdb=" CG2 ILE F 143 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 3833 not shown) Planarity restraints: 4197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 212 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 213 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 162 " 0.037 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP C 162 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP C 162 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 162 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 162 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 162 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 162 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 162 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 162 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 162 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 172 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C ARG G 172 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG G 172 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP G 173 " 0.021 2.00e-02 2.50e+03 ... (remaining 4194 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 10 2.23 - 2.90: 8749 2.90 - 3.57: 32284 3.57 - 4.23: 48424 4.23 - 4.90: 81176 Nonbonded interactions: 170643 Sorted by model distance: nonbonded pdb=" CZ3 TRP J 906 " pdb=" O ILE J1095 " model vdw 1.563 3.340 nonbonded pdb=" CE3 TRP J 906 " pdb=" O ILE J1095 " model vdw 1.741 3.340 nonbonded pdb=" NH1 ARG D 19 " pdb=" O ALA D 24 " model vdw 2.017 3.120 nonbonded pdb=" OH TYR D 4 " pdb=" OD2 ASP D 93 " model vdw 2.030 3.040 nonbonded pdb=" OD2 ASP J 478 " pdb=" CE1 PHE J 488 " model vdw 2.070 3.340 ... (remaining 170638 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 8 through 189) selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.020 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 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 : 0.007 0.079 23692 Z= 0.366 Angle : 1.440 23.705 32235 Z= 0.806 Chirality : 0.076 0.495 3836 Planarity : 0.008 0.103 4197 Dihedral : 14.416 90.588 7909 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.99 % Favored : 89.14 % Rotamer: Outliers : 0.69 % Allowed : 1.19 % Favored : 98.12 % Cbeta Deviations : 0.09 % 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: -4.65 (0.11), residues: 3233 helix: -2.69 (0.11), residues: 1083 sheet: -2.44 (0.20), residues: 579 loop : -3.67 (0.12), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG B 87 TYR 0.048 0.004 TYR J 905 PHE 0.047 0.004 PHE H 95 TRP 0.060 0.003 TRP C 162 HIS 0.011 0.002 HIS J1126 Details of bonding type rmsd covalent geometry : bond 0.00688 (23692) covalent geometry : angle 1.44043 (32235) hydrogen bonds : bond 0.18187 ( 952) hydrogen bonds : angle 8.38487 ( 2739) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 449 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.5126 (tpt) cc_final: 0.4874 (tpt) REVERT: A 75 PHE cc_start: 0.8448 (m-80) cc_final: 0.8079 (m-80) REVERT: C 45 TYR cc_start: 0.4538 (m-10) cc_final: 0.4246 (m-10) REVERT: C 59 MET cc_start: 0.8305 (tpp) cc_final: 0.7918 (tpp) REVERT: B 140 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: B 187 LEU cc_start: 0.7020 (tp) cc_final: 0.6782 (tp) REVERT: D 35 LYS cc_start: 0.6916 (pttm) cc_final: 0.6592 (pttm) REVERT: D 139 LYS cc_start: 0.7292 (tmtt) cc_final: 0.6891 (mttp) REVERT: D 141 THR cc_start: 0.6694 (t) cc_final: 0.6171 (t) REVERT: E 132 TYR cc_start: 0.6000 (t80) cc_final: 0.5377 (t80) REVERT: G 169 MET cc_start: 0.7519 (mmp) cc_final: 0.6798 (mmm) REVERT: H 40 ILE cc_start: 0.8813 (pt) cc_final: 0.8581 (pt) REVERT: H 113 MET cc_start: 0.8143 (tmm) cc_final: 0.7780 (tmm) REVERT: J 519 GLU cc_start: 0.6271 (tt0) cc_final: 0.6042 (tt0) REVERT: J 651 PRO cc_start: 0.8976 (Cg_endo) cc_final: 0.8729 (Cg_exo) REVERT: J 739 PHE cc_start: 0.6614 (t80) cc_final: 0.6371 (t80) REVERT: J 808 LEU cc_start: 0.6431 (pp) cc_final: 0.5824 (tp) REVERT: J 821 ARG cc_start: 0.6144 (ppt170) cc_final: 0.5566 (ptt90) REVERT: J 1041 LEU cc_start: 0.7876 (mt) cc_final: 0.7606 (mp) REVERT: J 1226 ARG cc_start: 0.7879 (pmt-80) cc_final: 0.7474 (pmt-80) REVERT: K 550 GLU cc_start: 0.7189 (tp30) cc_final: 0.6818 (tm-30) outliers start: 14 outliers final: 2 residues processed: 458 average time/residue: 0.1667 time to fit residues: 116.7544 Evaluate side-chains 258 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 255 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain J residue 907 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 156 GLN B 94 HIS B 143 ASN E 23 ASN E 56 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 485 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.081377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.071087 restraints weight = 135439.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.072333 restraints weight = 86383.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.072955 restraints weight = 58180.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.073072 restraints weight = 48876.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.073209 restraints weight = 45378.471| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23692 Z= 0.166 Angle : 0.723 10.596 32235 Z= 0.384 Chirality : 0.046 0.186 3836 Planarity : 0.005 0.067 4197 Dihedral : 6.250 48.193 3461 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.93 % Favored : 89.89 % Rotamer: Outliers : 2.03 % Allowed : 11.78 % Favored : 86.19 % 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: -3.40 (0.13), residues: 3233 helix: -0.76 (0.14), residues: 1102 sheet: -2.18 (0.21), residues: 592 loop : -3.52 (0.13), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 181 TYR 0.053 0.002 TYR H 96 PHE 0.027 0.002 PHE H 95 TRP 0.015 0.002 TRP C 162 HIS 0.004 0.001 HIS I 997 Details of bonding type rmsd covalent geometry : bond 0.00361 (23692) covalent geometry : angle 0.72297 (32235) hydrogen bonds : bond 0.04505 ( 952) hydrogen bonds : angle 5.80895 ( 2739) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.7257 (t80) cc_final: 0.7022 (t80) REVERT: B 50 ASN cc_start: 0.7709 (m110) cc_final: 0.7416 (m110) REVERT: B 140 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: B 166 LYS cc_start: 0.8565 (tptt) cc_final: 0.8119 (tttt) REVERT: B 187 LEU cc_start: 0.7337 (tp) cc_final: 0.7125 (tp) REVERT: D 12 HIS cc_start: 0.6294 (m-70) cc_final: 0.5997 (m170) REVERT: D 66 ASP cc_start: 0.8321 (m-30) cc_final: 0.8120 (m-30) REVERT: G 53 LYS cc_start: 0.8206 (ptpp) cc_final: 0.7791 (ptmt) REVERT: H 91 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7302 (pptt) REVERT: J 538 MET cc_start: 0.8438 (ttm) cc_final: 0.8202 (ttp) REVERT: J 821 ARG cc_start: 0.6040 (ppt170) cc_final: 0.5556 (ptt90) REVERT: J 907 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7519 (mptt) REVERT: J 909 MET cc_start: 0.6279 (tmm) cc_final: 0.6000 (tmm) REVERT: K 429 MET cc_start: 0.7056 (ttm) cc_final: 0.6775 (mtp) REVERT: K 550 GLU cc_start: 0.7899 (tp30) cc_final: 0.7073 (tm-30) outliers start: 41 outliers final: 19 residues processed: 295 average time/residue: 0.1387 time to fit residues: 66.4952 Evaluate side-chains 250 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 CYS Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain J residue 732 THR Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain K residue 422 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 270 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 178 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 292 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 228 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.080960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.070763 restraints weight = 134894.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.071960 restraints weight = 83797.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.072745 restraints weight = 56817.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.072833 restraints weight = 47295.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.072944 restraints weight = 41959.272| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23692 Z= 0.139 Angle : 0.657 9.555 32235 Z= 0.344 Chirality : 0.045 0.240 3836 Planarity : 0.004 0.057 4197 Dihedral : 5.675 45.440 3459 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.02 % Favored : 89.79 % Rotamer: Outliers : 1.68 % Allowed : 15.34 % Favored : 82.98 % 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: -2.78 (0.14), residues: 3233 helix: 0.12 (0.15), residues: 1102 sheet: -1.97 (0.21), residues: 610 loop : -3.40 (0.13), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 993 TYR 0.042 0.001 TYR H 96 PHE 0.037 0.002 PHE H 95 TRP 0.023 0.001 TRP C 162 HIS 0.004 0.001 HIS K 490 Details of bonding type rmsd covalent geometry : bond 0.00301 (23692) covalent geometry : angle 0.65680 (32235) hydrogen bonds : bond 0.03911 ( 952) hydrogen bonds : angle 5.25854 ( 2739) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8588 (tt0) cc_final: 0.8308 (tp40) REVERT: B 50 ASN cc_start: 0.7658 (m110) cc_final: 0.7423 (m110) REVERT: G 53 LYS cc_start: 0.8100 (ptpp) cc_final: 0.7742 (pttt) REVERT: J 821 ARG cc_start: 0.6004 (ppt170) cc_final: 0.5503 (ptt90) REVERT: J 907 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7762 (mptt) REVERT: K 429 MET cc_start: 0.6857 (ttm) cc_final: 0.6580 (mtp) REVERT: K 550 GLU cc_start: 0.7811 (tp30) cc_final: 0.7127 (tm-30) outliers start: 34 outliers final: 16 residues processed: 280 average time/residue: 0.1400 time to fit residues: 64.7070 Evaluate side-chains 240 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 732 THR Chi-restraints excluded: chain J residue 907 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 22 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 183 optimal weight: 0.3980 chunk 149 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN H 94 HIS H 120 ASN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 486 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.080121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.070045 restraints weight = 135204.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.071162 restraints weight = 85066.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.071773 restraints weight = 58612.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.071889 restraints weight = 49404.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.071974 restraints weight = 45810.688| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 23692 Z= 0.152 Angle : 0.646 8.404 32235 Z= 0.340 Chirality : 0.045 0.176 3836 Planarity : 0.004 0.056 4197 Dihedral : 5.429 40.956 3457 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.30 % Favored : 89.45 % Rotamer: Outliers : 2.38 % Allowed : 17.62 % Favored : 80.01 % 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: -2.50 (0.14), residues: 3233 helix: 0.53 (0.16), residues: 1100 sheet: -1.96 (0.21), residues: 605 loop : -3.32 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 181 TYR 0.028 0.002 TYR B 45 PHE 0.026 0.002 PHE J1037 TRP 0.023 0.002 TRP J 649 HIS 0.004 0.001 HIS K 490 Details of bonding type rmsd covalent geometry : bond 0.00342 (23692) covalent geometry : angle 0.64572 (32235) hydrogen bonds : bond 0.03751 ( 952) hydrogen bonds : angle 5.03459 ( 2739) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 59 MET cc_start: 0.8605 (tpp) cc_final: 0.8398 (tpp) REVERT: D 12 HIS cc_start: 0.6197 (m-70) cc_final: 0.5714 (m170) REVERT: E 148 MET cc_start: 0.1798 (ttp) cc_final: 0.1591 (ttp) REVERT: G 169 MET cc_start: 0.6447 (mmm) cc_final: 0.6233 (mmm) REVERT: G 192 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: J 821 ARG cc_start: 0.6044 (ppt170) cc_final: 0.5568 (ptt90) REVERT: J 907 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7750 (mmtm) REVERT: J 1000 MET cc_start: 0.6831 (tpt) cc_final: 0.6571 (tpt) REVERT: K 429 MET cc_start: 0.6790 (ttm) cc_final: 0.6426 (mtp) REVERT: K 550 GLU cc_start: 0.7833 (tp30) cc_final: 0.7126 (tm-30) outliers start: 48 outliers final: 30 residues processed: 282 average time/residue: 0.1265 time to fit residues: 59.9457 Evaluate side-chains 255 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain G residue 192 PHE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain J residue 732 THR Chi-restraints excluded: chain J residue 743 PHE Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1022 VAL Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 489 LEU Chi-restraints excluded: chain K residue 540 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 235 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 173 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 209 optimal weight: 0.0470 chunk 311 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 233 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN H 94 HIS ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1141 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.080025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.069977 restraints weight = 134108.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.071087 restraints weight = 84983.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.071844 restraints weight = 58649.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.071908 restraints weight = 48036.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.071964 restraints weight = 44190.969| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23692 Z= 0.147 Angle : 0.639 10.078 32235 Z= 0.335 Chirality : 0.044 0.182 3836 Planarity : 0.004 0.058 4197 Dihedral : 5.305 44.771 3457 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.33 % Favored : 89.42 % Rotamer: Outliers : 2.28 % Allowed : 19.89 % Favored : 77.83 % 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: -2.34 (0.15), residues: 3233 helix: 0.76 (0.16), residues: 1101 sheet: -1.94 (0.21), residues: 611 loop : -3.28 (0.14), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 181 TYR 0.033 0.001 TYR H 103 PHE 0.026 0.001 PHE J1037 TRP 0.025 0.001 TRP J 649 HIS 0.004 0.001 HIS K 490 Details of bonding type rmsd covalent geometry : bond 0.00328 (23692) covalent geometry : angle 0.63880 (32235) hydrogen bonds : bond 0.03622 ( 952) hydrogen bonds : angle 4.89681 ( 2739) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.5949 (tm-30) REVERT: B 134 LEU cc_start: 0.9075 (mt) cc_final: 0.8774 (mt) REVERT: E 219 GLN cc_start: 0.5429 (pp30) cc_final: 0.5164 (pp30) REVERT: G 192 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: H 103 TYR cc_start: 0.6443 (t80) cc_final: 0.6128 (t80) REVERT: H 136 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7802 (pm20) REVERT: J 732 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7569 (p) REVERT: J 821 ARG cc_start: 0.6040 (ppt170) cc_final: 0.5567 (ptt90) REVERT: J 907 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7899 (mmtm) REVERT: K 429 MET cc_start: 0.6818 (ttm) cc_final: 0.6475 (mtp) REVERT: K 550 GLU cc_start: 0.7827 (tp30) cc_final: 0.7183 (tm-30) outliers start: 46 outliers final: 26 residues processed: 273 average time/residue: 0.1271 time to fit residues: 58.8911 Evaluate side-chains 248 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 162 TRP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 192 PHE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 732 THR Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1009 PHE Chi-restraints excluded: chain J residue 1022 VAL Chi-restraints excluded: chain K residue 422 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 259 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 188 optimal weight: 0.0000 chunk 53 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 103 ASN D 56 GLN D 142 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 432 GLN K 486 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.077967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.068069 restraints weight = 137644.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.069296 restraints weight = 83073.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.069593 restraints weight = 57703.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.069755 restraints weight = 53584.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.069790 restraints weight = 47396.885| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23692 Z= 0.222 Angle : 0.713 8.875 32235 Z= 0.378 Chirality : 0.046 0.187 3836 Planarity : 0.004 0.060 4197 Dihedral : 5.740 55.999 3457 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.91 % Favored : 87.84 % Rotamer: Outliers : 2.77 % Allowed : 21.23 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.15), residues: 3233 helix: 0.71 (0.16), residues: 1108 sheet: -1.94 (0.21), residues: 594 loop : -3.38 (0.14), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 181 TYR 0.029 0.002 TYR J 619 PHE 0.032 0.002 PHE F 49 TRP 0.031 0.002 TRP J 649 HIS 0.006 0.001 HIS K 490 Details of bonding type rmsd covalent geometry : bond 0.00494 (23692) covalent geometry : angle 0.71345 (32235) hydrogen bonds : bond 0.04144 ( 952) hydrogen bonds : angle 5.21381 ( 2739) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 ARG cc_start: 0.5526 (ttt90) cc_final: 0.5125 (ttm-80) REVERT: D 22 THR cc_start: 0.7061 (OUTLIER) cc_final: 0.6684 (p) REVERT: E 219 GLN cc_start: 0.5407 (pp30) cc_final: 0.5152 (pp30) REVERT: J 821 ARG cc_start: 0.6019 (ppt170) cc_final: 0.5507 (ptt90) REVERT: J 907 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7843 (mmtm) REVERT: J 1125 GLU cc_start: 0.6943 (tt0) cc_final: 0.6620 (tm-30) REVERT: J 1204 GLN cc_start: 0.6814 (mm110) cc_final: 0.6502 (mp10) REVERT: K 429 MET cc_start: 0.6950 (ttm) cc_final: 0.6570 (mtp) REVERT: K 550 GLU cc_start: 0.7825 (tp30) cc_final: 0.7346 (tm-30) outliers start: 56 outliers final: 33 residues processed: 265 average time/residue: 0.1317 time to fit residues: 58.8488 Evaluate side-chains 252 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 162 TRP Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 905 TYR Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1022 VAL Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain J residue 1194 THR Chi-restraints excluded: chain J residue 1211 LEU Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 527 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 88 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 228 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 256 optimal weight: 0.0370 chunk 257 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 62 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN H 94 HIS ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.079828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.069997 restraints weight = 135702.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.071023 restraints weight = 78875.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.071659 restraints weight = 56643.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.071773 restraints weight = 49190.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.071798 restraints weight = 43028.723| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23692 Z= 0.124 Angle : 0.651 12.579 32235 Z= 0.336 Chirality : 0.045 0.521 3836 Planarity : 0.004 0.059 4197 Dihedral : 5.215 47.917 3457 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.19 % Favored : 90.57 % Rotamer: Outliers : 1.83 % Allowed : 23.06 % Favored : 75.11 % 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: -2.13 (0.15), residues: 3233 helix: 1.03 (0.16), residues: 1101 sheet: -1.80 (0.22), residues: 594 loop : -3.25 (0.14), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 181 TYR 0.034 0.001 TYR H 96 PHE 0.029 0.001 PHE C 30 TRP 0.027 0.001 TRP J 649 HIS 0.003 0.001 HIS I 997 Details of bonding type rmsd covalent geometry : bond 0.00271 (23692) covalent geometry : angle 0.65121 (32235) hydrogen bonds : bond 0.03514 ( 952) hydrogen bonds : angle 4.77850 ( 2739) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8331 (m-80) cc_final: 0.7994 (m-80) REVERT: D 22 THR cc_start: 0.7130 (OUTLIER) cc_final: 0.6907 (p) REVERT: F 115 PHE cc_start: 0.8222 (p90) cc_final: 0.8016 (p90) REVERT: J 538 MET cc_start: 0.8169 (mtp) cc_final: 0.7965 (mtp) REVERT: J 821 ARG cc_start: 0.5976 (ppt170) cc_final: 0.5504 (ptt90) REVERT: J 907 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7898 (mmtm) REVERT: K 429 MET cc_start: 0.6993 (ttm) cc_final: 0.6626 (mtp) REVERT: K 550 GLU cc_start: 0.7818 (tp30) cc_final: 0.7271 (tm-30) outliers start: 37 outliers final: 22 residues processed: 275 average time/residue: 0.1359 time to fit residues: 62.1517 Evaluate side-chains 246 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 498 PHE Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 743 PHE Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1009 PHE Chi-restraints excluded: chain J residue 1274 ASP Chi-restraints excluded: chain K residue 422 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 62 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 257 optimal weight: 10.0000 chunk 310 optimal weight: 30.0000 chunk 182 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 268 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.078582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.068784 restraints weight = 135422.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.069826 restraints weight = 81148.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.070406 restraints weight = 58285.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.070525 restraints weight = 51832.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.070561 restraints weight = 44648.734| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23692 Z= 0.178 Angle : 0.692 14.975 32235 Z= 0.357 Chirality : 0.046 0.237 3836 Planarity : 0.004 0.060 4197 Dihedral : 5.370 54.405 3457 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.63 % Favored : 88.09 % Rotamer: Outliers : 2.13 % Allowed : 23.65 % Favored : 74.22 % 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: -2.20 (0.15), residues: 3233 helix: 1.00 (0.16), residues: 1105 sheet: -1.91 (0.21), residues: 606 loop : -3.30 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 181 TYR 0.037 0.002 TYR H 96 PHE 0.030 0.002 PHE F 49 TRP 0.030 0.002 TRP J 649 HIS 0.005 0.001 HIS K 490 Details of bonding type rmsd covalent geometry : bond 0.00402 (23692) covalent geometry : angle 0.69231 (32235) hydrogen bonds : bond 0.03762 ( 952) hydrogen bonds : angle 4.89912 ( 2739) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 THR cc_start: 0.7185 (OUTLIER) cc_final: 0.6829 (p) REVERT: F 115 PHE cc_start: 0.8268 (p90) cc_final: 0.8018 (p90) REVERT: G 169 MET cc_start: 0.6963 (mmp) cc_final: 0.6749 (mmp) REVERT: J 754 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7831 (mm) REVERT: J 821 ARG cc_start: 0.5974 (ppt170) cc_final: 0.5497 (ptt90) REVERT: J 907 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7939 (mmtm) REVERT: K 429 MET cc_start: 0.6984 (ttm) cc_final: 0.6648 (mtp) REVERT: K 550 GLU cc_start: 0.7657 (tp30) cc_final: 0.7322 (tm-30) outliers start: 43 outliers final: 31 residues processed: 250 average time/residue: 0.1341 time to fit residues: 56.5406 Evaluate side-chains 244 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 162 TRP Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 836 ILE Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 905 TYR Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1009 PHE Chi-restraints excluded: chain J residue 1013 VAL Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain J residue 1194 THR Chi-restraints excluded: chain J residue 1274 ASP Chi-restraints excluded: chain K residue 422 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 285 optimal weight: 0.0170 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.0670 chunk 124 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 313 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN H 94 HIS ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.079523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.069788 restraints weight = 135510.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.070764 restraints weight = 78487.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.071388 restraints weight = 57383.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.071517 restraints weight = 49304.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.071592 restraints weight = 43125.287| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23692 Z= 0.134 Angle : 0.683 17.641 32235 Z= 0.346 Chirality : 0.045 0.357 3836 Planarity : 0.004 0.063 4197 Dihedral : 5.162 50.586 3457 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.87 % Favored : 89.89 % Rotamer: Outliers : 1.93 % Allowed : 24.00 % Favored : 74.07 % 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: -2.09 (0.15), residues: 3233 helix: 1.10 (0.16), residues: 1104 sheet: -1.80 (0.21), residues: 599 loop : -3.26 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 181 TYR 0.033 0.001 TYR H 96 PHE 0.020 0.001 PHE C 30 TRP 0.028 0.001 TRP J 649 HIS 0.004 0.001 HIS H 172 Details of bonding type rmsd covalent geometry : bond 0.00302 (23692) covalent geometry : angle 0.68341 (32235) hydrogen bonds : bond 0.03553 ( 952) hydrogen bonds : angle 4.74546 ( 2739) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8339 (m-80) cc_final: 0.8021 (m-80) REVERT: D 22 THR cc_start: 0.7220 (OUTLIER) cc_final: 0.6957 (p) REVERT: F 115 PHE cc_start: 0.8245 (p90) cc_final: 0.8001 (p90) REVERT: J 821 ARG cc_start: 0.5928 (ppt170) cc_final: 0.5453 (ptt90) REVERT: J 907 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7938 (mmtm) REVERT: K 429 MET cc_start: 0.6966 (ttm) cc_final: 0.6621 (mtp) REVERT: K 550 GLU cc_start: 0.7645 (tp30) cc_final: 0.7289 (tm-30) outliers start: 39 outliers final: 28 residues processed: 251 average time/residue: 0.1288 time to fit residues: 55.1310 Evaluate side-chains 242 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 836 ILE Chi-restraints excluded: chain J residue 498 PHE Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1009 PHE Chi-restraints excluded: chain J residue 1013 VAL Chi-restraints excluded: chain J residue 1274 ASP Chi-restraints excluded: chain K residue 422 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 66 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 321 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 230 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 319 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.079484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.069621 restraints weight = 136174.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.070695 restraints weight = 80413.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.071349 restraints weight = 57738.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.071459 restraints weight = 50144.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.071499 restraints weight = 43294.850| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 23692 Z= 0.161 Angle : 0.803 59.193 32235 Z= 0.428 Chirality : 0.045 0.343 3836 Planarity : 0.004 0.062 4197 Dihedral : 5.181 50.540 3457 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.24 % Favored : 89.51 % Rotamer: Outliers : 1.63 % Allowed : 24.20 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.09 (0.15), residues: 3233 helix: 1.11 (0.16), residues: 1104 sheet: -1.85 (0.21), residues: 605 loop : -3.24 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.033 0.001 TYR H 96 PHE 0.017 0.001 PHE C 30 TRP 0.028 0.001 TRP J 649 HIS 0.011 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00357 (23692) covalent geometry : angle 0.80306 (32235) hydrogen bonds : bond 0.03551 ( 952) hydrogen bonds : angle 4.74474 ( 2739) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8346 (m-80) cc_final: 0.8028 (m-80) REVERT: B 157 MET cc_start: 0.7519 (mmp) cc_final: 0.7060 (mmm) REVERT: D 22 THR cc_start: 0.7225 (OUTLIER) cc_final: 0.6963 (p) REVERT: F 115 PHE cc_start: 0.8242 (p90) cc_final: 0.8004 (p90) REVERT: J 821 ARG cc_start: 0.5902 (ppt170) cc_final: 0.5425 (ptt90) REVERT: J 907 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7939 (mmtm) REVERT: K 429 MET cc_start: 0.6955 (ttm) cc_final: 0.6608 (mtp) REVERT: K 550 GLU cc_start: 0.7649 (tp30) cc_final: 0.7291 (tm-30) outliers start: 33 outliers final: 29 residues processed: 236 average time/residue: 0.1285 time to fit residues: 51.8271 Evaluate side-chains 244 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 836 ILE Chi-restraints excluded: chain J residue 498 PHE Chi-restraints excluded: chain J residue 649 TRP Chi-restraints excluded: chain J residue 750 LEU Chi-restraints excluded: chain J residue 907 LYS Chi-restraints excluded: chain J residue 1009 PHE Chi-restraints excluded: chain J residue 1013 VAL Chi-restraints excluded: chain J residue 1038 ILE Chi-restraints excluded: chain J residue 1274 ASP Chi-restraints excluded: chain K residue 422 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 103 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 0.1980 chunk 298 optimal weight: 4.9990 chunk 280 optimal weight: 0.8980 chunk 225 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 259 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.079500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.069514 restraints weight = 134963.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.070631 restraints weight = 83503.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.071258 restraints weight = 57349.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.071357 restraints weight = 47891.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.071404 restraints weight = 44409.874| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 23692 Z= 0.161 Angle : 0.803 59.193 32235 Z= 0.428 Chirality : 0.045 0.343 3836 Planarity : 0.004 0.062 4197 Dihedral : 5.181 50.540 3457 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.24 % Favored : 89.51 % Rotamer: Outliers : 1.53 % Allowed : 24.29 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.09 (0.15), residues: 3233 helix: 1.11 (0.16), residues: 1104 sheet: -1.85 (0.21), residues: 605 loop : -3.24 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.033 0.001 TYR H 96 PHE 0.017 0.001 PHE C 30 TRP 0.028 0.001 TRP J 649 HIS 0.011 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00357 (23692) covalent geometry : angle 0.80306 (32235) hydrogen bonds : bond 0.03551 ( 952) hydrogen bonds : angle 4.74474 ( 2739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3847.45 seconds wall clock time: 67 minutes 3.66 seconds (4023.66 seconds total)