Starting phenix.real_space_refine on Thu Mar 5 15:16:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3a_25652/03_2026/7t3a_25652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3a_25652/03_2026/7t3a_25652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t3a_25652/03_2026/7t3a_25652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3a_25652/03_2026/7t3a_25652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t3a_25652/03_2026/7t3a_25652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3a_25652/03_2026/7t3a_25652.map" } resolution = 4.0 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 131 5.16 5 C 14912 2.51 5 N 3942 2.21 5 O 4322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s 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: 23310 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 8120 Classifications: {'peptide': 990} Link IDs: {'PTRANS': 41, 'TRANS': 948} Chain breaks: 7 Chain: "B" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2926 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "C" Number of atoms: 3242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3242 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 385} Chain breaks: 5 Chain: "K" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2416 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 5, 'TRANS': 288} Chain: "L" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2420 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain: "M" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 940 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 918 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 111} Chain: "P" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 738 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "Q" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 666 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.98, per 1000 atoms: 0.21 Number of scatterers: 23310 At special positions: 0 Unit cell: (123.795, 159.165, 233.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 3 15.00 O 4322 8.00 N 3942 7.00 C 14912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS K 124 " - pdb=" SG CYS K 159 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 23 sheets defined 39.6% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 92 through 96 removed outlier: 3.643A pdb=" N VAL A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 96 " --> pdb=" O LYS A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 96' Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.717A pdb=" N TRP A 182 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.402A pdb=" N THR A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.926A pdb=" N ASP A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 762 through 769 removed outlier: 3.897A pdb=" N ASP A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 removed outlier: 3.928A pdb=" N ALA A 781 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP A 782 " --> pdb=" O PRO A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 809 removed outlier: 3.635A pdb=" N VAL A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 800 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 809 " --> pdb=" O GLN A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 928 removed outlier: 3.507A pdb=" N LEU A 921 " --> pdb=" O LYS A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 940 removed outlier: 3.913A pdb=" N LYS A 940 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 removed outlier: 3.529A pdb=" N THR A 956 " --> pdb=" O CYS A 952 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A 958 " --> pdb=" O THR A 954 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 994 removed outlier: 5.107A pdb=" N GLN A 981 " --> pdb=" O GLU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1186 removed outlier: 4.295A pdb=" N HIS A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1218 Processing helix chain 'A' and resid 1223 through 1237 removed outlier: 3.734A pdb=" N ALA A1227 " --> pdb=" O THR A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1291 removed outlier: 3.517A pdb=" N ARG A1291 " --> pdb=" O ALA A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1291' Processing helix chain 'A' and resid 1309 through 1313 removed outlier: 3.565A pdb=" N LEU A1312 " --> pdb=" O PRO A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1411 Processing helix chain 'A' and resid 1445 through 1449 Processing helix chain 'A' and resid 1461 through 1463 No H-bonds generated for 'chain 'A' and resid 1461 through 1463' Processing helix chain 'A' and resid 1464 through 1480 Processing helix chain 'A' and resid 1567 through 1581 Processing helix chain 'A' and resid 1582 through 1584 No H-bonds generated for 'chain 'A' and resid 1582 through 1584' Processing helix chain 'A' and resid 1585 through 1596 Processing helix chain 'A' and resid 1597 through 1599 No H-bonds generated for 'chain 'A' and resid 1597 through 1599' Processing helix chain 'B' and resid 97 through 117 removed outlier: 4.343A pdb=" N ILE B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Proline residue: B 130 - end of helix Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.900A pdb=" N PHE B 184 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.562A pdb=" N ASP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 293 through 301 removed outlier: 3.564A pdb=" N HIS B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 318 removed outlier: 4.047A pdb=" N ILE B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 361 through 370 removed outlier: 5.004A pdb=" N GLU B 367 " --> pdb=" O HIS B 363 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.716A pdb=" N MET C 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS C 80 " --> pdb=" O SER C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 80' Processing helix chain 'C' and resid 135 through 160 Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.156A pdb=" N ARG C 165 " --> pdb=" O GLN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 removed outlier: 3.888A pdb=" N CYS C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 274 Processing helix chain 'C' and resid 279 through 288 removed outlier: 3.563A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 305 through 320 removed outlier: 3.596A pdb=" N GLY C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 356 removed outlier: 4.128A pdb=" N GLN C 351 " --> pdb=" O PRO C 347 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 368 Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.527A pdb=" N GLU C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 removed outlier: 3.625A pdb=" N SER C 489 " --> pdb=" O ASN C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.551A pdb=" N ARG C 495 " --> pdb=" O SER C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 516 removed outlier: 3.527A pdb=" N LEU C 510 " --> pdb=" O ASN C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 520 Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 536 through 547 Processing helix chain 'C' and resid 558 through 564 removed outlier: 4.345A pdb=" N ALA C 562 " --> pdb=" O ASP C 558 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 28 removed outlier: 4.208A pdb=" N ARG K 24 " --> pdb=" O LYS K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 66 through 76 Processing helix chain 'K' and resid 77 through 83 removed outlier: 3.538A pdb=" N PHE K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG K 83 " --> pdb=" O ASP K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 117 Processing helix chain 'K' and resid 128 through 132 removed outlier: 4.159A pdb=" N LEU K 131 " --> pdb=" O LYS K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 152 Processing helix chain 'K' and resid 167 through 181 removed outlier: 3.782A pdb=" N LYS K 171 " --> pdb=" O GLU K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 199 removed outlier: 3.691A pdb=" N LEU K 187 " --> pdb=" O ASN K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 243 Processing helix chain 'K' and resid 244 through 246 No H-bonds generated for 'chain 'K' and resid 244 through 246' Processing helix chain 'K' and resid 283 through 297 Processing helix chain 'L' and resid 73 through 86 removed outlier: 3.831A pdb=" N ILE L 77 " --> pdb=" O GLY L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 111 removed outlier: 3.842A pdb=" N SER L 105 " --> pdb=" O LYS L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 130 Processing helix chain 'L' and resid 149 through 161 removed outlier: 4.612A pdb=" N HIS L 158 " --> pdb=" O LEU L 154 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE L 159 " --> pdb=" O THR L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 168 Processing helix chain 'L' and resid 184 through 199 Processing helix chain 'L' and resid 199 through 204 removed outlier: 3.658A pdb=" N ALA L 204 " --> pdb=" O ASN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 235 removed outlier: 4.054A pdb=" N ALA L 228 " --> pdb=" O SER L 224 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS L 235 " --> pdb=" O LYS L 231 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 251 removed outlier: 3.566A pdb=" N LEU L 243 " --> pdb=" O GLN L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 300 removed outlier: 3.859A pdb=" N LEU L 284 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL L 295 " --> pdb=" O VAL L 291 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR L 299 " --> pdb=" O VAL L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 358 removed outlier: 3.959A pdb=" N TYR L 354 " --> pdb=" O GLY L 350 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN L 355 " --> pdb=" O LEU L 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 64 Processing helix chain 'M' and resid 78 through 95 removed outlier: 3.709A pdb=" N ASP M 83 " --> pdb=" O HIS M 79 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU M 95 " --> pdb=" O ARG M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 120 removed outlier: 3.645A pdb=" N VAL M 118 " --> pdb=" O GLN M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 142 removed outlier: 3.515A pdb=" N LEU M 129 " --> pdb=" O PRO M 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 43 through 45 No H-bonds generated for 'chain 'N' and resid 43 through 45' Processing helix chain 'N' and resid 46 through 59 removed outlier: 3.988A pdb=" N SER N 50 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA N 54 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG N 58 " --> pdb=" O ALA N 54 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN N 59 " --> pdb=" O ALA N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 Processing helix chain 'N' and resid 117 through 124 Processing helix chain 'O' and resid 4 through 12 Processing helix chain 'O' and resid 13 through 16 Processing helix chain 'O' and resid 41 through 45 Processing helix chain 'O' and resid 46 through 60 removed outlier: 4.172A pdb=" N LEU O 50 " --> pdb=" O ARG O 46 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE O 53 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA O 54 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA O 56 " --> pdb=" O THR O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 110 Processing helix chain 'O' and resid 111 through 113 No H-bonds generated for 'chain 'O' and resid 111 through 113' Processing helix chain 'O' and resid 114 through 120 removed outlier: 3.520A pdb=" N ARG O 118 " --> pdb=" O PHE O 114 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN O 119 " --> pdb=" O GLU O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 12 removed outlier: 4.015A pdb=" N ILE P 12 " --> pdb=" O LEU P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 51 Processing helix chain 'Q' and resid 2 through 13 removed outlier: 3.580A pdb=" N GLU Q 6 " --> pdb=" O GLU Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 53 removed outlier: 4.698A pdb=" N GLY Q 43 " --> pdb=" O ASP Q 39 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL Q 44 " --> pdb=" O GLU Q 40 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA Q 53 " --> pdb=" O ALA Q 49 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.900A pdb=" N ILE A 67 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER A 57 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 25 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 134 removed outlier: 6.014A pdb=" N GLU A 101 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU A 144 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU A 99 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 100 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 163 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 367 removed outlier: 7.957A pdb=" N VAL A 364 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER A 333 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU A 366 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL A 335 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N MET A 170 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL A 334 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR A 172 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE A 336 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE A 174 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR A 255 " --> pdb=" O CYS A 893 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 382 removed outlier: 4.286A pdb=" N ASP A 396 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 770 through 777 Processing sheet with id=AA7, first strand: chain 'A' and resid 1351 through 1357 removed outlier: 6.869A pdb=" N GLU A1385 " --> pdb=" O HIS A1375 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG A 945 " --> pdb=" O VAL A1419 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A1419 " --> pdb=" O ARG A 945 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1204 through 1206 Processing sheet with id=AA9, first strand: chain 'A' and resid 1254 through 1255 removed outlier: 6.824A pdb=" N ALA A1297 " --> pdb=" O PHE A1378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1439 through 1442 removed outlier: 5.212A pdb=" N VAL A1509 " --> pdb=" O HIS A1504 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN A1501 " --> pdb=" O ASP A1485 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 22 through 26 removed outlier: 5.051A pdb=" N ILE B 23 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU B 14 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ILE B 7 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASP B 90 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 62 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 145 through 148 Processing sheet with id=AB4, first strand: chain 'B' and resid 174 through 177 Processing sheet with id=AB5, first strand: chain 'B' and resid 245 through 247 Processing sheet with id=AB6, first strand: chain 'B' and resid 328 through 329 Processing sheet with id=AB7, first strand: chain 'C' and resid 22 through 26 removed outlier: 4.703A pdb=" N LEU C 22 " --> pdb=" O SER C 14 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 14 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 260 through 263 Processing sheet with id=AB9, first strand: chain 'C' and resid 372 through 373 removed outlier: 5.183A pdb=" N VAL C 333 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 45 through 52 removed outlier: 6.897A pdb=" N LYS K 8 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N TRP K 61 " --> pdb=" O LYS K 8 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL K 10 " --> pdb=" O TRP K 61 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS K 63 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU K 12 " --> pdb=" O CYS K 63 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE K 122 " --> pdb=" O ALA K 158 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE K 160 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N CYS K 124 " --> pdb=" O PHE K 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 213 through 218 removed outlier: 6.867A pdb=" N VAL K 213 " --> pdb=" O GLU K 207 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU K 207 " --> pdb=" O VAL K 213 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 64 through 65 removed outlier: 3.630A pdb=" N LEU L 65 " --> pdb=" O ALA L 139 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE L 141 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU L 140 " --> pdb=" O GLU L 174 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE L 176 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR L 142 " --> pdb=" O PHE L 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'N' and resid 31 through 36 removed outlier: 6.525A pdb=" N LEU N 24 " --> pdb=" O LEU N 32 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR N 34 " --> pdb=" O THR N 22 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR N 22 " --> pdb=" O TYR N 34 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL N 81 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE O 72 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL O 80 " --> pdb=" O CYS O 73 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N SER O 95 " --> pdb=" O LEU O 19 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU O 19 " --> pdb=" O SER O 95 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE O 22 " --> pdb=" O LYS O 34 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS O 34 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL O 24 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 25 through 29 removed outlier: 6.588A pdb=" N VAL P 20 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER P 29 " --> pdb=" O TYR P 18 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR P 18 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS P 88 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR P 18 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL P 86 " --> pdb=" O TYR P 18 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL P 20 " --> pdb=" O VAL P 84 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL P 84 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG P 65 " --> pdb=" O GLU Q 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL Q 86 " --> pdb=" O MET Q 75 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN Q 77 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA Q 85 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2697 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: 5.47 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7565 1.35 - 1.48: 5839 1.48 - 1.61: 10202 1.61 - 1.74: 4 1.74 - 1.87: 197 Bond restraints: 23807 Sorted by residual: bond pdb=" C VAL A 733 " pdb=" N PRO A 734 " ideal model delta sigma weight residual 1.337 1.414 -0.077 9.80e-03 1.04e+04 6.22e+01 bond pdb=" C GLU N 117 " pdb=" N PRO N 118 " ideal model delta sigma weight residual 1.336 1.399 -0.064 1.23e-02 6.61e+03 2.67e+01 bond pdb=" C ASP L 125 " pdb=" N PRO L 126 " ideal model delta sigma weight residual 1.336 1.398 -0.062 1.23e-02 6.61e+03 2.54e+01 bond pdb=" N3B GNP K 500 " pdb=" PG GNP K 500 " ideal model delta sigma weight residual 1.801 1.703 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O5' GNP K 500 " pdb=" PA GNP K 500 " ideal model delta sigma weight residual 1.660 1.570 0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 23802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 31443 3.34 - 6.69: 653 6.69 - 10.03: 131 10.03 - 13.38: 15 13.38 - 16.72: 6 Bond angle restraints: 32248 Sorted by residual: angle pdb=" C PHE K 52 " pdb=" N LEU K 53 " pdb=" CA LEU K 53 " ideal model delta sigma weight residual 122.46 130.46 -8.00 1.41e+00 5.03e-01 3.22e+01 angle pdb=" N VAL A 733 " pdb=" CA VAL A 733 " pdb=" C VAL A 733 " ideal model delta sigma weight residual 108.88 120.92 -12.04 2.16e+00 2.14e-01 3.11e+01 angle pdb=" C GLU C 226 " pdb=" N VAL C 227 " pdb=" CA VAL C 227 " ideal model delta sigma weight residual 120.62 129.73 -9.11 1.64e+00 3.72e-01 3.08e+01 angle pdb=" C GLU A 288 " pdb=" N GLN A 289 " pdb=" CA GLN A 289 " ideal model delta sigma weight residual 122.61 131.03 -8.42 1.56e+00 4.11e-01 2.91e+01 angle pdb=" CB MET K 252 " pdb=" CG MET K 252 " pdb=" SD MET K 252 " ideal model delta sigma weight residual 112.70 128.59 -15.89 3.00e+00 1.11e-01 2.81e+01 ... (remaining 32243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 12477 17.39 - 34.78: 1542 34.78 - 52.18: 260 52.18 - 69.57: 54 69.57 - 86.96: 26 Dihedral angle restraints: 14359 sinusoidal: 5830 harmonic: 8529 Sorted by residual: dihedral pdb=" CA VAL A 258 " pdb=" C VAL A 258 " pdb=" N VAL A 259 " pdb=" CA VAL A 259 " ideal model delta harmonic sigma weight residual -180.00 -123.04 -56.96 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA VAL N 86 " pdb=" C VAL N 86 " pdb=" N ALA N 87 " pdb=" CA ALA N 87 " ideal model delta harmonic sigma weight residual -180.00 -131.18 -48.82 0 5.00e+00 4.00e-02 9.53e+01 dihedral pdb=" CA VAL L 264 " pdb=" C VAL L 264 " pdb=" N VAL L 265 " pdb=" CA VAL L 265 " ideal model delta harmonic sigma weight residual -180.00 -140.70 -39.30 0 5.00e+00 4.00e-02 6.18e+01 ... (remaining 14356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3269 0.103 - 0.207: 348 0.207 - 0.310: 25 0.310 - 0.414: 3 0.414 - 0.517: 2 Chirality restraints: 3647 Sorted by residual: chirality pdb=" CB ILE L 237 " pdb=" CA ILE L 237 " pdb=" CG1 ILE L 237 " pdb=" CG2 ILE L 237 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CB ILE C 324 " pdb=" CA ILE C 324 " pdb=" CG1 ILE C 324 " pdb=" CG2 ILE C 324 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CB ILE K 181 " pdb=" CA ILE K 181 " pdb=" CG1 ILE K 181 " pdb=" CG2 ILE K 181 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 3644 not shown) Planarity restraints: 4109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 106 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" CG ASP A 106 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASP A 106 " 0.026 2.00e-02 2.50e+03 pdb=" OD2 ASP A 106 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 282 " -0.019 2.00e-02 2.50e+03 2.62e-02 1.21e+01 pdb=" CG PHE B 282 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 282 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE B 282 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 282 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 282 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 282 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 305 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ASN A 305 " -0.060 2.00e-02 2.50e+03 pdb=" O ASN A 305 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR A 306 " 0.020 2.00e-02 2.50e+03 ... (remaining 4106 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4079 2.77 - 3.30: 21366 3.30 - 3.83: 39614 3.83 - 4.37: 43185 4.37 - 4.90: 72981 Nonbonded interactions: 181225 Sorted by model distance: nonbonded pdb=" OG1 THR A 864 " pdb=" OG1 THR A 871 " model vdw 2.234 3.040 nonbonded pdb=" O THR A 217 " pdb=" OG1 THR A 217 " model vdw 2.253 3.040 nonbonded pdb=" OG SER B 187 " pdb=" OE1 GLN B 188 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR P 74 " pdb=" OD1 ASN P 91 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR B 241 " pdb=" OE2 GLU B 310 " model vdw 2.287 3.040 ... (remaining 181220 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.850 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.990 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 23810 Z= 0.288 Angle : 1.198 16.722 32250 Z= 0.615 Chirality : 0.065 0.517 3647 Planarity : 0.007 0.069 4109 Dihedral : 15.610 86.959 8808 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.26 % Favored : 90.71 % Rotamer: Outliers : 0.04 % Allowed : 1.16 % Favored : 98.80 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.22 (0.14), residues: 2851 helix: -2.24 (0.13), residues: 1004 sheet: -1.38 (0.22), residues: 534 loop : -2.29 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 193 TYR 0.034 0.003 TYR B 351 PHE 0.060 0.003 PHE B 282 TRP 0.045 0.002 TRP M 102 HIS 0.017 0.002 HIS A1375 Details of bonding type rmsd covalent geometry : bond 0.00611 (23807) covalent geometry : angle 1.19687 (32248) SS BOND : bond 0.01388 ( 1) SS BOND : angle 5.43554 ( 2) hydrogen bonds : bond 0.14927 ( 960) hydrogen bonds : angle 7.64193 ( 2697) Misc. bond : bond 0.00442 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8596 (pmm) cc_final: 0.8258 (pmm) REVERT: B 255 VAL cc_start: 0.8637 (t) cc_final: 0.8220 (p) REVERT: B 319 MET cc_start: 0.8309 (mmp) cc_final: 0.8099 (mmm) REVERT: B 329 TYR cc_start: 0.7799 (m-80) cc_final: 0.7554 (m-80) REVERT: B 360 MET cc_start: 0.8202 (tpt) cc_final: 0.7965 (tpp) REVERT: C 79 MET cc_start: 0.8424 (mpp) cc_final: 0.8080 (mpp) REVERT: C 89 ASP cc_start: 0.8292 (p0) cc_final: 0.7842 (m-30) REVERT: C 90 ASN cc_start: 0.8696 (p0) cc_final: 0.8394 (p0) REVERT: C 308 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8291 (tm-30) REVERT: C 368 PHE cc_start: 0.9245 (m-80) cc_final: 0.9043 (m-80) REVERT: K 139 LEU cc_start: 0.9398 (tt) cc_final: 0.9172 (mm) REVERT: K 273 MET cc_start: 0.9160 (tpt) cc_final: 0.8936 (tpt) REVERT: L 67 MET cc_start: 0.2688 (pmm) cc_final: 0.2263 (pmm) REVERT: L 192 GLN cc_start: 0.8921 (pp30) cc_final: 0.8491 (pp30) REVERT: L 288 MET cc_start: 0.9142 (tmm) cc_final: 0.8851 (tmm) REVERT: L 294 ASP cc_start: 0.8419 (p0) cc_final: 0.8197 (p0) REVERT: M 88 TYR cc_start: 0.7918 (m-10) cc_final: 0.7584 (m-80) REVERT: O 79 GLN cc_start: 0.7763 (mp10) cc_final: 0.7240 (mp10) REVERT: O 109 GLU cc_start: 0.8549 (tp30) cc_final: 0.7891 (pt0) REVERT: Q 24 THR cc_start: 0.7128 (t) cc_final: 0.6791 (t) REVERT: Q 37 LEU cc_start: 0.6536 (mt) cc_final: 0.6327 (mt) outliers start: 1 outliers final: 1 residues processed: 318 average time/residue: 0.1510 time to fit residues: 76.7041 Evaluate side-chains 230 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 30 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN A 797 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1216 ASN A1484 GLN B 205 HIS K 186 GLN L 83 HIS L 212 HIS ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN N 15 ASN Q 7 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.092610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.072164 restraints weight = 109828.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.072101 restraints weight = 59051.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.072661 restraints weight = 54301.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.072721 restraints weight = 45746.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.073136 restraints weight = 41543.390| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23810 Z= 0.161 Angle : 0.717 10.895 32250 Z= 0.372 Chirality : 0.046 0.194 3647 Planarity : 0.004 0.056 4109 Dihedral : 6.895 56.660 3162 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.72 % Favored : 92.25 % Rotamer: Outliers : 0.85 % Allowed : 9.26 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.17 (0.15), residues: 2851 helix: -0.78 (0.15), residues: 1008 sheet: -1.11 (0.23), residues: 520 loop : -2.06 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 46 TYR 0.022 0.002 TYR L 299 PHE 0.022 0.001 PHE B 282 TRP 0.022 0.001 TRP B 379 HIS 0.007 0.001 HIS Q 79 Details of bonding type rmsd covalent geometry : bond 0.00352 (23807) covalent geometry : angle 0.71647 (32248) SS BOND : bond 0.03123 ( 1) SS BOND : angle 1.42148 ( 2) hydrogen bonds : bond 0.04390 ( 960) hydrogen bonds : angle 5.79226 ( 2697) Misc. bond : bond 0.00200 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8625 (pmm) cc_final: 0.8140 (pmm) REVERT: A 1184 MET cc_start: 0.7926 (ptp) cc_final: 0.7691 (mtm) REVERT: A 1553 MET cc_start: 0.8344 (ptm) cc_final: 0.7940 (ptp) REVERT: A 1598 MET cc_start: 0.7249 (ptp) cc_final: 0.6949 (ptp) REVERT: B 182 GLU cc_start: 0.8511 (pp20) cc_final: 0.8278 (pp20) REVERT: B 208 LYS cc_start: 0.5336 (OUTLIER) cc_final: 0.4692 (ttmt) REVERT: B 226 ASN cc_start: 0.8620 (t160) cc_final: 0.8337 (t0) REVERT: B 323 ILE cc_start: 0.9189 (mm) cc_final: 0.8773 (tp) REVERT: B 329 TYR cc_start: 0.8058 (m-80) cc_final: 0.7639 (m-80) REVERT: C 79 MET cc_start: 0.8455 (mpp) cc_final: 0.8244 (mpp) REVERT: C 125 ASN cc_start: 0.8371 (t0) cc_final: 0.7859 (m110) REVERT: C 312 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8675 (pt) REVERT: C 368 PHE cc_start: 0.9162 (m-80) cc_final: 0.8930 (m-80) REVERT: K 23 MET cc_start: 0.8495 (ptp) cc_final: 0.8155 (mtt) REVERT: L 132 MET cc_start: 0.8256 (ttt) cc_final: 0.7949 (tpp) REVERT: L 288 MET cc_start: 0.8879 (tmm) cc_final: 0.8660 (tmm) REVERT: M 88 TYR cc_start: 0.7935 (m-10) cc_final: 0.7680 (m-80) REVERT: N 37 TYR cc_start: 0.5261 (p90) cc_final: 0.4879 (p90) REVERT: O 109 GLU cc_start: 0.8453 (tp30) cc_final: 0.7988 (pt0) REVERT: Q 24 THR cc_start: 0.8024 (t) cc_final: 0.7618 (t) outliers start: 22 outliers final: 11 residues processed: 264 average time/residue: 0.1338 time to fit residues: 58.5609 Evaluate side-chains 230 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain M residue 57 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 148 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 270 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 GLN A 809 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS Q 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.090750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.070621 restraints weight = 109656.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.070579 restraints weight = 61012.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.070940 restraints weight = 52311.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.071123 restraints weight = 43976.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.071222 restraints weight = 41244.907| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 23810 Z= 0.226 Angle : 0.726 9.321 32250 Z= 0.377 Chirality : 0.046 0.188 3647 Planarity : 0.004 0.050 4109 Dihedral : 6.423 57.638 3160 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.77 % Favored : 91.20 % Rotamer: Outliers : 1.81 % Allowed : 13.66 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.16), residues: 2851 helix: -0.24 (0.16), residues: 1012 sheet: -1.06 (0.23), residues: 523 loop : -1.96 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 193 TYR 0.023 0.002 TYR L 299 PHE 0.026 0.002 PHE B 11 TRP 0.020 0.002 TRP B 379 HIS 0.006 0.001 HIS P 56 Details of bonding type rmsd covalent geometry : bond 0.00491 (23807) covalent geometry : angle 0.72572 (32248) SS BOND : bond 0.00551 ( 1) SS BOND : angle 1.14155 ( 2) hydrogen bonds : bond 0.04154 ( 960) hydrogen bonds : angle 5.61543 ( 2697) Misc. bond : bond 0.00206 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8667 (pmm) cc_final: 0.8134 (pmm) REVERT: B 208 LYS cc_start: 0.5108 (OUTLIER) cc_final: 0.4442 (ttmt) REVERT: B 226 ASN cc_start: 0.8638 (t160) cc_final: 0.8284 (t0) REVERT: B 323 ILE cc_start: 0.9134 (mm) cc_final: 0.8815 (tp) REVERT: C 312 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8674 (pt) REVERT: C 393 MET cc_start: 0.8850 (mmm) cc_final: 0.8608 (mmp) REVERT: K 47 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8680 (p-80) REVERT: L 132 MET cc_start: 0.8210 (ttt) cc_final: 0.7922 (tpp) REVERT: M 88 TYR cc_start: 0.7947 (m-10) cc_final: 0.7655 (m-80) outliers start: 47 outliers final: 28 residues processed: 261 average time/residue: 0.1356 time to fit residues: 58.2173 Evaluate side-chains 243 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 13 MET Chi-restraints excluded: chain Q residue 30 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 257 optimal weight: 30.0000 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 274 optimal weight: 30.0000 chunk 148 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.090965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071180 restraints weight = 109177.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.070229 restraints weight = 70239.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.070410 restraints weight = 59432.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.070706 restraints weight = 55686.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.071064 restraints weight = 45473.014| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23810 Z= 0.167 Angle : 0.678 9.115 32250 Z= 0.350 Chirality : 0.045 0.184 3647 Planarity : 0.004 0.056 4109 Dihedral : 6.163 58.773 3160 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.07 % Favored : 91.90 % Rotamer: Outliers : 1.97 % Allowed : 16.29 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.16), residues: 2851 helix: -0.01 (0.16), residues: 1017 sheet: -1.01 (0.23), residues: 516 loop : -1.90 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 422 TYR 0.021 0.002 TYR L 130 PHE 0.019 0.001 PHE K 259 TRP 0.019 0.001 TRP B 379 HIS 0.014 0.001 HIS A1375 Details of bonding type rmsd covalent geometry : bond 0.00370 (23807) covalent geometry : angle 0.67772 (32248) SS BOND : bond 0.00262 ( 1) SS BOND : angle 0.80915 ( 2) hydrogen bonds : bond 0.03834 ( 960) hydrogen bonds : angle 5.48874 ( 2697) Misc. bond : bond 0.00179 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7864 (t0) cc_final: 0.7622 (t0) REVERT: A 1598 MET cc_start: 0.7001 (ptp) cc_final: 0.6791 (ptp) REVERT: B 208 LYS cc_start: 0.5082 (OUTLIER) cc_final: 0.4396 (tttt) REVERT: B 226 ASN cc_start: 0.8590 (t160) cc_final: 0.8145 (t0) REVERT: B 323 ILE cc_start: 0.9126 (mm) cc_final: 0.8815 (tp) REVERT: B 329 TYR cc_start: 0.8286 (m-80) cc_final: 0.8032 (m-80) REVERT: C 312 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8707 (pt) REVERT: K 23 MET cc_start: 0.8415 (ptp) cc_final: 0.8093 (mtt) REVERT: K 47 HIS cc_start: 0.8969 (OUTLIER) cc_final: 0.8656 (p-80) REVERT: M 88 TYR cc_start: 0.7936 (m-10) cc_final: 0.7646 (m-80) REVERT: M 134 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6040 (pmt-80) REVERT: O 79 GLN cc_start: 0.7674 (mp10) cc_final: 0.7070 (mp10) REVERT: O 109 GLU cc_start: 0.8507 (tp30) cc_final: 0.8018 (tt0) outliers start: 51 outliers final: 31 residues processed: 265 average time/residue: 0.1504 time to fit residues: 64.9193 Evaluate side-chains 249 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 276 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 1 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 147 optimal weight: 0.3980 chunk 91 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS P 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.090449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.070381 restraints weight = 108126.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.069426 restraints weight = 69354.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.069996 restraints weight = 53104.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.070131 restraints weight = 50434.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.070859 restraints weight = 41716.491| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23810 Z= 0.185 Angle : 0.689 10.107 32250 Z= 0.353 Chirality : 0.046 0.213 3647 Planarity : 0.004 0.053 4109 Dihedral : 6.059 58.218 3160 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.35 % Allowed : 17.17 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.16), residues: 2851 helix: 0.11 (0.16), residues: 1025 sheet: -1.03 (0.23), residues: 518 loop : -1.90 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 422 TYR 0.020 0.002 TYR L 299 PHE 0.031 0.002 PHE B 11 TRP 0.017 0.001 TRP B 379 HIS 0.010 0.001 HIS A1375 Details of bonding type rmsd covalent geometry : bond 0.00410 (23807) covalent geometry : angle 0.68860 (32248) SS BOND : bond 0.00259 ( 1) SS BOND : angle 0.81831 ( 2) hydrogen bonds : bond 0.03803 ( 960) hydrogen bonds : angle 5.47499 ( 2697) Misc. bond : bond 0.00160 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8045 (t0) cc_final: 0.7702 (t0) REVERT: B 208 LYS cc_start: 0.5218 (OUTLIER) cc_final: 0.4508 (tttt) REVERT: B 329 TYR cc_start: 0.8286 (m-80) cc_final: 0.8038 (m-80) REVERT: C 73 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.9012 (mm) REVERT: C 312 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8748 (pt) REVERT: C 393 MET cc_start: 0.8887 (mmm) cc_final: 0.8666 (mmm) REVERT: K 47 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8552 (p-80) REVERT: L 67 MET cc_start: 0.2778 (pmm) cc_final: 0.2027 (pmm) REVERT: M 88 TYR cc_start: 0.7930 (m-10) cc_final: 0.7625 (m-80) REVERT: M 134 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6107 (pmt-80) REVERT: O 109 GLU cc_start: 0.8530 (tp30) cc_final: 0.7993 (tt0) REVERT: Q 75 MET cc_start: 0.7145 (mmt) cc_final: 0.6498 (mmp) outliers start: 61 outliers final: 40 residues processed: 259 average time/residue: 0.1392 time to fit residues: 59.3838 Evaluate side-chains 249 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 13 MET Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 209 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 93 optimal weight: 0.0770 chunk 275 optimal weight: 8.9990 chunk 281 optimal weight: 20.0000 chunk 213 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 overall best weight: 2.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 226 ASN ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS Q 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.091120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071266 restraints weight = 109010.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.070285 restraints weight = 68361.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.070668 restraints weight = 57224.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.070905 restraints weight = 55646.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.071178 restraints weight = 43827.161| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23810 Z= 0.152 Angle : 0.676 10.201 32250 Z= 0.345 Chirality : 0.045 0.184 3647 Planarity : 0.004 0.055 4109 Dihedral : 5.895 56.537 3160 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.28 % Allowed : 18.68 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.16), residues: 2851 helix: 0.26 (0.17), residues: 1020 sheet: -1.02 (0.23), residues: 515 loop : -1.85 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 85 TYR 0.019 0.002 TYR L 165 PHE 0.023 0.001 PHE B 11 TRP 0.014 0.001 TRP C 319 HIS 0.014 0.001 HIS A1375 Details of bonding type rmsd covalent geometry : bond 0.00340 (23807) covalent geometry : angle 0.67564 (32248) SS BOND : bond 0.00231 ( 1) SS BOND : angle 0.76057 ( 2) hydrogen bonds : bond 0.03678 ( 960) hydrogen bonds : angle 5.36839 ( 2697) Misc. bond : bond 0.00175 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8447 (t0) cc_final: 0.8053 (t0) REVERT: A 1553 MET cc_start: 0.8482 (ptm) cc_final: 0.8203 (ptt) REVERT: A 1598 MET cc_start: 0.7490 (ptp) cc_final: 0.7229 (ptp) REVERT: B 63 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8588 (mtpt) REVERT: B 208 LYS cc_start: 0.5393 (OUTLIER) cc_final: 0.4714 (tttt) REVERT: B 319 MET cc_start: 0.8175 (mmm) cc_final: 0.7852 (mmm) REVERT: B 323 ILE cc_start: 0.9237 (tp) cc_final: 0.8895 (tp) REVERT: C 73 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9040 (mm) REVERT: C 312 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8870 (pt) REVERT: C 393 MET cc_start: 0.8997 (mmm) cc_final: 0.8774 (mmp) REVERT: K 23 MET cc_start: 0.8617 (ptp) cc_final: 0.8329 (mtt) REVERT: K 47 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8598 (p-80) REVERT: L 67 MET cc_start: 0.2613 (pmm) cc_final: 0.2202 (pmm) REVERT: L 140 LEU cc_start: 0.8905 (mm) cc_final: 0.8688 (mm) REVERT: M 88 TYR cc_start: 0.7911 (m-10) cc_final: 0.7611 (m-80) REVERT: M 134 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6235 (pmt-80) REVERT: N 56 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: O 109 GLU cc_start: 0.8589 (tp30) cc_final: 0.8006 (tt0) outliers start: 59 outliers final: 39 residues processed: 266 average time/residue: 0.1408 time to fit residues: 61.4892 Evaluate side-chains 250 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 159 CYS Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 276 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 56 TYR Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 30 ASN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 88 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 205 HIS B 226 ASN ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS Q 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.090966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.071038 restraints weight = 108249.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.069894 restraints weight = 68847.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.070350 restraints weight = 55084.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.070492 restraints weight = 51165.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.071143 restraints weight = 43163.023| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23810 Z= 0.160 Angle : 0.685 10.025 32250 Z= 0.349 Chirality : 0.045 0.184 3647 Planarity : 0.004 0.054 4109 Dihedral : 5.835 56.142 3160 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.66 % Allowed : 19.30 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.16), residues: 2851 helix: 0.33 (0.17), residues: 1018 sheet: -1.04 (0.23), residues: 507 loop : -1.81 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 85 TYR 0.019 0.001 TYR L 165 PHE 0.022 0.001 PHE B 282 TRP 0.012 0.001 TRP M 102 HIS 0.017 0.001 HIS A1375 Details of bonding type rmsd covalent geometry : bond 0.00359 (23807) covalent geometry : angle 0.68535 (32248) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.80259 ( 2) hydrogen bonds : bond 0.03675 ( 960) hydrogen bonds : angle 5.34651 ( 2697) Misc. bond : bond 0.00164 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8088 (mp0) cc_final: 0.7804 (mp0) REVERT: A 1553 MET cc_start: 0.8429 (ptm) cc_final: 0.8083 (ptp) REVERT: A 1598 MET cc_start: 0.7523 (ptp) cc_final: 0.7315 (ptp) REVERT: B 208 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.4744 (tttt) REVERT: B 319 MET cc_start: 0.8356 (mmm) cc_final: 0.8137 (mmm) REVERT: B 323 ILE cc_start: 0.9293 (tp) cc_final: 0.8935 (tp) REVERT: B 329 TYR cc_start: 0.8404 (m-80) cc_final: 0.8159 (m-80) REVERT: C 377 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6976 (m-10) REVERT: C 393 MET cc_start: 0.9004 (mmm) cc_final: 0.8740 (mmp) REVERT: K 23 MET cc_start: 0.8621 (ptp) cc_final: 0.8368 (mtt) REVERT: K 47 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8371 (p-80) REVERT: K 168 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8144 (p) REVERT: L 67 MET cc_start: 0.2678 (pmm) cc_final: 0.2416 (pmm) REVERT: L 140 LEU cc_start: 0.8882 (mm) cc_final: 0.8638 (mm) REVERT: M 88 TYR cc_start: 0.7913 (m-10) cc_final: 0.7610 (m-80) REVERT: M 134 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6226 (pmt-80) REVERT: N 56 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: Q 75 MET cc_start: 0.7096 (mmt) cc_final: 0.6560 (mmp) outliers start: 69 outliers final: 48 residues processed: 263 average time/residue: 0.1389 time to fit residues: 60.1958 Evaluate side-chains 258 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1417 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 159 CYS Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 276 MET Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 56 TYR Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 246 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 167 optimal weight: 30.0000 chunk 89 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 154 optimal weight: 30.0000 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 226 ASN ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 190 ASN K 250 GLN ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS Q 30 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.090304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.070277 restraints weight = 107904.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.069099 restraints weight = 72869.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.069538 restraints weight = 56855.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.069931 restraints weight = 46980.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.070255 restraints weight = 41544.974| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 23810 Z= 0.192 Angle : 0.718 13.897 32250 Z= 0.364 Chirality : 0.046 0.188 3647 Planarity : 0.004 0.055 4109 Dihedral : 5.877 55.480 3160 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.78 % Allowed : 20.38 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.16), residues: 2851 helix: 0.33 (0.17), residues: 1020 sheet: -1.04 (0.23), residues: 514 loop : -1.82 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 193 TYR 0.018 0.002 TYR L 165 PHE 0.019 0.001 PHE B 11 TRP 0.012 0.001 TRP A1548 HIS 0.017 0.001 HIS A1375 Details of bonding type rmsd covalent geometry : bond 0.00428 (23807) covalent geometry : angle 0.71749 (32248) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.84452 ( 2) hydrogen bonds : bond 0.03783 ( 960) hydrogen bonds : angle 5.43517 ( 2697) Misc. bond : bond 0.00166 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 207 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8802 (m-30) cc_final: 0.8278 (t0) REVERT: A 180 GLU cc_start: 0.8098 (mp0) cc_final: 0.7795 (mp0) REVERT: A 1553 MET cc_start: 0.8478 (ptm) cc_final: 0.8160 (ptp) REVERT: B 137 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8321 (pm20) REVERT: B 208 LYS cc_start: 0.5384 (OUTLIER) cc_final: 0.4649 (tttt) REVERT: B 319 MET cc_start: 0.8412 (mmm) cc_final: 0.8158 (mmm) REVERT: B 323 ILE cc_start: 0.9331 (tp) cc_final: 0.8988 (tp) REVERT: B 329 TYR cc_start: 0.8448 (m-80) cc_final: 0.8156 (m-80) REVERT: C 377 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6999 (m-10) REVERT: C 393 MET cc_start: 0.9036 (mmm) cc_final: 0.8801 (mmp) REVERT: K 47 HIS cc_start: 0.8971 (OUTLIER) cc_final: 0.8304 (p-80) REVERT: K 168 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8138 (p) REVERT: L 67 MET cc_start: 0.2693 (pmm) cc_final: 0.2466 (pmm) REVERT: L 140 LEU cc_start: 0.8886 (mm) cc_final: 0.8633 (mm) REVERT: M 88 TYR cc_start: 0.7923 (m-10) cc_final: 0.7599 (m-80) REVERT: M 134 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6232 (pmt-80) REVERT: N 56 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: O 75 TYR cc_start: 0.7567 (m-80) cc_final: 0.6978 (m-80) REVERT: O 109 GLU cc_start: 0.8821 (tp30) cc_final: 0.8244 (tt0) REVERT: Q 75 MET cc_start: 0.7040 (mmt) cc_final: 0.6497 (mmp) outliers start: 72 outliers final: 54 residues processed: 256 average time/residue: 0.1306 time to fit residues: 55.3517 Evaluate side-chains 261 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1417 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 159 CYS Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 276 MET Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 56 TYR Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 30 ASN Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 248 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 271 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 268 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 226 ASN ** C 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 GLN ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.092190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.072335 restraints weight = 109075.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.071252 restraints weight = 65843.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.071740 restraints weight = 54034.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.071934 restraints weight = 50498.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.072517 restraints weight = 41983.609| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23810 Z= 0.126 Angle : 0.709 14.098 32250 Z= 0.356 Chirality : 0.046 0.301 3647 Planarity : 0.003 0.054 4109 Dihedral : 5.657 54.798 3160 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.59 % Allowed : 20.88 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.16), residues: 2851 helix: 0.45 (0.17), residues: 1011 sheet: -0.84 (0.24), residues: 497 loop : -1.76 (0.18), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 85 TYR 0.021 0.001 TYR L 165 PHE 0.032 0.001 PHE N 101 TRP 0.026 0.001 TRP M 102 HIS 0.011 0.001 HIS A1375 Details of bonding type rmsd covalent geometry : bond 0.00281 (23807) covalent geometry : angle 0.70854 (32248) SS BOND : bond 0.00206 ( 1) SS BOND : angle 0.79964 ( 2) hydrogen bonds : bond 0.03606 ( 960) hydrogen bonds : angle 5.30980 ( 2697) Misc. bond : bond 0.00172 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7838 (mp0) cc_final: 0.7629 (mp0) REVERT: A 1553 MET cc_start: 0.8101 (ptm) cc_final: 0.7889 (ptt) REVERT: B 208 LYS cc_start: 0.5419 (OUTLIER) cc_final: 0.4656 (tttt) REVERT: B 323 ILE cc_start: 0.9228 (tp) cc_final: 0.8924 (tp) REVERT: B 329 TYR cc_start: 0.8208 (m-80) cc_final: 0.7936 (m-80) REVERT: C 377 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6920 (m-10) REVERT: C 393 MET cc_start: 0.8950 (mmm) cc_final: 0.8697 (mmp) REVERT: K 47 HIS cc_start: 0.8708 (OUTLIER) cc_final: 0.7971 (p-80) REVERT: K 168 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7811 (p) REVERT: K 239 LYS cc_start: 0.9410 (tppt) cc_final: 0.9188 (tppt) REVERT: L 67 MET cc_start: 0.3026 (pmm) cc_final: 0.2794 (pmm) REVERT: L 130 TYR cc_start: 0.1694 (p90) cc_final: 0.1099 (m-10) REVERT: L 140 LEU cc_start: 0.8693 (mm) cc_final: 0.8438 (mm) REVERT: M 88 TYR cc_start: 0.7873 (m-10) cc_final: 0.7571 (m-80) REVERT: M 134 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6189 (pmt-80) REVERT: N 37 TYR cc_start: 0.5182 (p90) cc_final: 0.4875 (p90) REVERT: N 56 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: O 75 TYR cc_start: 0.7126 (m-80) cc_final: 0.6609 (m-80) REVERT: Q 37 LEU cc_start: 0.5023 (mt) cc_final: 0.4599 (mt) REVERT: Q 75 MET cc_start: 0.7109 (mmt) cc_final: 0.6569 (mmp) outliers start: 67 outliers final: 43 residues processed: 276 average time/residue: 0.1332 time to fit residues: 60.9361 Evaluate side-chains 261 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 159 CYS Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 276 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 56 TYR Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 262 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN K 250 GLN ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.091838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.071973 restraints weight = 109248.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.070885 restraints weight = 66426.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.071506 restraints weight = 53684.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.071645 restraints weight = 50692.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.072312 restraints weight = 41671.846| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23810 Z= 0.142 Angle : 0.728 14.199 32250 Z= 0.365 Chirality : 0.046 0.283 3647 Planarity : 0.003 0.056 4109 Dihedral : 5.602 55.032 3160 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.08 % Allowed : 21.65 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.16), residues: 2851 helix: 0.47 (0.17), residues: 1018 sheet: -0.84 (0.24), residues: 496 loop : -1.76 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 193 TYR 0.020 0.001 TYR A 775 PHE 0.027 0.001 PHE N 101 TRP 0.029 0.001 TRP M 102 HIS 0.014 0.001 HIS A1375 Details of bonding type rmsd covalent geometry : bond 0.00320 (23807) covalent geometry : angle 0.72804 (32248) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.84821 ( 2) hydrogen bonds : bond 0.03662 ( 960) hydrogen bonds : angle 5.36137 ( 2697) Misc. bond : bond 0.00169 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 213 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8039 (mp0) cc_final: 0.7738 (mp0) REVERT: A 1553 MET cc_start: 0.8360 (ptm) cc_final: 0.8022 (ptp) REVERT: B 177 PHE cc_start: 0.7674 (t80) cc_final: 0.7472 (t80) REVERT: B 310 GLU cc_start: 0.8798 (pm20) cc_final: 0.8208 (pp20) REVERT: B 323 ILE cc_start: 0.9320 (tp) cc_final: 0.8994 (tp) REVERT: B 329 TYR cc_start: 0.8381 (m-80) cc_final: 0.8120 (m-80) REVERT: C 377 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6882 (m-10) REVERT: C 393 MET cc_start: 0.9028 (mmm) cc_final: 0.8758 (mmp) REVERT: K 47 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.7974 (p-80) REVERT: K 168 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8066 (p) REVERT: K 224 ASP cc_start: 0.8431 (p0) cc_final: 0.8163 (p0) REVERT: L 67 MET cc_start: 0.2929 (pmm) cc_final: 0.2706 (pmm) REVERT: L 130 TYR cc_start: 0.1811 (p90) cc_final: 0.1119 (m-10) REVERT: L 140 LEU cc_start: 0.8748 (mm) cc_final: 0.8478 (mm) REVERT: M 88 TYR cc_start: 0.7876 (m-10) cc_final: 0.7566 (m-80) REVERT: M 134 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6262 (pmt-80) REVERT: N 37 TYR cc_start: 0.5218 (p90) cc_final: 0.4907 (p90) REVERT: N 56 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: O 75 TYR cc_start: 0.7497 (m-80) cc_final: 0.6886 (m-80) REVERT: Q 13 MET cc_start: 0.4624 (mtt) cc_final: 0.4408 (mtm) REVERT: Q 75 MET cc_start: 0.7026 (mmt) cc_final: 0.6489 (mmp) outliers start: 54 outliers final: 45 residues processed: 252 average time/residue: 0.1404 time to fit residues: 58.2581 Evaluate side-chains 260 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 1189 THR Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 159 CYS Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 276 MET Chi-restraints excluded: chain K residue 286 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 56 TYR Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 224 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 280 optimal weight: 20.0000 chunk 174 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN K 250 GLN K 289 ASN ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** 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 = 0.3930 r_free = 0.3930 target = 0.092655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.072390 restraints weight = 108423.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.071927 restraints weight = 63684.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.072312 restraints weight = 48847.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.072594 restraints weight = 47790.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.072767 restraints weight = 39853.250| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23810 Z= 0.126 Angle : 0.723 13.607 32250 Z= 0.360 Chirality : 0.046 0.287 3647 Planarity : 0.003 0.055 4109 Dihedral : 5.444 54.717 3160 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.08 % Allowed : 21.61 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.16), residues: 2851 helix: 0.52 (0.17), residues: 1019 sheet: -0.84 (0.23), residues: 507 loop : -1.70 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 193 TYR 0.022 0.001 TYR A 775 PHE 0.031 0.001 PHE B 282 TRP 0.028 0.001 TRP M 102 HIS 0.012 0.001 HIS A1375 Details of bonding type rmsd covalent geometry : bond 0.00281 (23807) covalent geometry : angle 0.72256 (32248) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.81944 ( 2) hydrogen bonds : bond 0.03550 ( 960) hydrogen bonds : angle 5.25645 ( 2697) Misc. bond : bond 0.00147 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3643.10 seconds wall clock time: 64 minutes 2.86 seconds (3842.86 seconds total)