Starting phenix.real_space_refine on Sun Oct 25 23:47:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lod_0936/10_2026/6lod_0936.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lod_0936/10_2026/6lod_0936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6lod_0936/10_2026/6lod_0936.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lod_0936/10_2026/6lod_0936.cif" model { file = "/net/cci-nas-00/data/ceres_data/6lod_0936/10_2026/6lod_0936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lod_0936/10_2026/6lod_0936.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lod_0936/10_2026/6lod_0936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lod_0936/10_2026/6lod_0936.map" } resolution = 3.2 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= 0.012 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 Fe 21 7.16 5 S 106 5.16 5 C 12235 2.51 5 N 3163 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18785 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1763 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "B" Number of atoms: 7176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7176 Classifications: {'peptide': 929} Link IDs: {'PTRANS': 54, 'TRANS': 874} Chain: "C" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3728 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 22, 'TRANS': 433} Chain: "D" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1348 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 13, 'TRANS': 160} Chain: "E" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1253 Unusual residues: {'ACE': 1} Classifications: {'peptide': 157, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 11, 'TRANS': 145} Chain: "F" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3159 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 100 Unusual residues: {'EL6': 1, 'F3S': 1, 'HEC': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'EL6': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7079 SG CYS B 772 43.538 61.115 46.899 1.00 15.91 S ATOM 8511 SG CYS B 952 43.881 60.933 52.417 1.00 17.30 S ATOM 7098 SG CYS B 775 48.859 61.179 48.961 1.00 14.45 S ATOM 7059 SG CYS B 769 45.917 56.117 49.454 1.00 17.48 S ATOM 8265 SG CYS B 921 54.211 68.702 54.752 1.00 12.95 S ATOM 8241 SG CYS B 918 57.243 63.355 54.147 1.00 16.80 S ATOM 7123 SG CYS B 779 55.518 66.495 50.074 1.00 15.00 S ATOM 8480 SG CYS B 948 51.626 64.350 54.163 1.00 15.65 S ATOM 7499 SG CYS B 824 61.983 60.284 55.837 1.00 13.73 S ATOM 7560 SG CYS B 832 67.745 58.412 56.225 1.00 13.23 S ATOM 7813 SG CYS B 866 65.347 56.019 52.750 1.00 13.66 S ATOM 7523 SG CYS B 827 63.465 55.132 58.459 1.00 14.54 S ATOM 7785 SG CYS B 862 71.717 60.915 50.750 1.00 14.21 S ATOM 7740 SG CYS B 856 72.937 66.254 49.471 1.00 13.76 S ATOM 7590 SG CYS B 836 74.814 63.418 54.435 1.00 13.58 S Time building chain proxies: 4.09, per 1000 atoms: 0.22 Number of scatterers: 18785 At special positions: 0 Unit cell: (159.12, 131.04, 97.76, 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) Fe 21 26.01 S 106 16.00 O 3260 8.00 N 3163 7.00 C 12235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 867.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B1106 " pdb="FE1 F3S B1106 " - pdb=" SG CYS B 862 " pdb="FE4 F3S B1106 " - pdb=" SG CYS B 836 " pdb="FE3 F3S B1106 " - pdb=" SG CYS B 856 " pdb=" SF4 B1103 " pdb="FE2 SF4 B1103 " - pdb=" SG CYS B 952 " pdb="FE1 SF4 B1103 " - pdb=" SG CYS B 772 " pdb="FE3 SF4 B1103 " - pdb=" SG CYS B 775 " pdb="FE4 SF4 B1103 " - pdb=" SG CYS B 769 " pdb=" SF4 B1104 " pdb="FE3 SF4 B1104 " - pdb=" SG CYS B 779 " pdb="FE1 SF4 B1104 " - pdb=" SG CYS B 921 " pdb="FE4 SF4 B1104 " - pdb=" SG CYS B 948 " pdb="FE2 SF4 B1104 " - pdb=" SG CYS B 918 " pdb=" SF4 B1105 " pdb="FE2 SF4 B1105 " - pdb=" SG CYS B 832 " pdb="FE4 SF4 B1105 " - pdb=" SG CYS B 827 " pdb="FE3 SF4 B1105 " - pdb=" SG CYS B 866 " pdb="FE1 SF4 B1105 " - pdb=" SG CYS B 824 " Number of angles added : 45 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4306 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 15 sheets defined 48.3% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 14 through 25 removed outlier: 3.693A pdb=" N LEU A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 43 Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.598A pdb=" N HIS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 4.201A pdb=" N CYS A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.523A pdb=" N SER A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 178 through 181 Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.608A pdb=" N VAL A 188 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 214 through 219 removed outlier: 3.669A pdb=" N THR A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.564A pdb=" N ALA B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.906A pdb=" N THR B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 191 removed outlier: 3.619A pdb=" N THR B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.603A pdb=" N THR B 217 " --> pdb=" O GLN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 removed outlier: 3.527A pdb=" N ALA B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.513A pdb=" N LEU B 280 " --> pdb=" O MET B 276 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 320 through 329 removed outlier: 3.599A pdb=" N ARG B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 removed outlier: 3.834A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 removed outlier: 3.707A pdb=" N ALA B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 removed outlier: 3.547A pdb=" N HIS B 378 " --> pdb=" O PRO B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 420 removed outlier: 3.723A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 462 through 467 removed outlier: 3.901A pdb=" N GLN B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 462 through 467' Processing helix chain 'B' and resid 506 through 516 removed outlier: 3.646A pdb=" N ASN B 512 " --> pdb=" O ILE B 508 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 538 through 550 Processing helix chain 'B' and resid 598 through 604 Processing helix chain 'B' and resid 620 through 628 Processing helix chain 'B' and resid 680 through 684 removed outlier: 3.568A pdb=" N ARG B 683 " --> pdb=" O ASN B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 733 Processing helix chain 'B' and resid 773 through 783 removed outlier: 3.500A pdb=" N VAL B 777 " --> pdb=" O ASN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'B' and resid 897 through 901 removed outlier: 3.645A pdb=" N MET B 901 " --> pdb=" O VAL B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 935 removed outlier: 3.525A pdb=" N GLU B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 928 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B 931 " --> pdb=" O GLU B 927 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 935 " --> pdb=" O GLN B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 973 removed outlier: 3.505A pdb=" N LEU B 972 " --> pdb=" O ARG B 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 16 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 52 through 71 removed outlier: 3.604A pdb=" N LEU C 56 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.938A pdb=" N VAL C 75 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TRP C 76 " --> pdb=" O VAL C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 76' Processing helix chain 'C' and resid 85 through 104 removed outlier: 3.898A pdb=" N PHE C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.597A pdb=" N PHE C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 133 removed outlier: 4.242A pdb=" N MET C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 144 through 152 removed outlier: 5.177A pdb=" N TYR C 149 " --> pdb=" O TRP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 190 removed outlier: 4.390A pdb=" N THR C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 214 removed outlier: 3.981A pdb=" N PHE C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 238 removed outlier: 4.104A pdb=" N ARG C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE C 233 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 255 removed outlier: 3.613A pdb=" N LEU C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N PHE C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 287 removed outlier: 3.824A pdb=" N VAL C 271 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 301 through 332 removed outlier: 4.328A pdb=" N VAL C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP C 330 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 349 through 362 removed outlier: 3.899A pdb=" N TYR C 353 " --> pdb=" O TYR C 349 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 362 " --> pdb=" O VAL C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 373 removed outlier: 4.018A pdb=" N TRP C 368 " --> pdb=" O GLN C 365 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS C 370 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG C 371 " --> pdb=" O TRP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 403 removed outlier: 3.919A pdb=" N PHE C 381 " --> pdb=" O PRO C 377 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.701A pdb=" N TRP C 411 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 442 removed outlier: 3.557A pdb=" N LEU C 423 " --> pdb=" O TRP C 419 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 428 " --> pdb=" O TYR C 424 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP C 430 " --> pdb=" O GLY C 426 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 434 " --> pdb=" O TRP C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 462 Processing helix chain 'D' and resid 33 through 42 removed outlier: 3.518A pdb=" N LYS D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 69 through 95 removed outlier: 3.649A pdb=" N LEU D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'E' and resid 98 through 112 removed outlier: 3.578A pdb=" N TYR E 112 " --> pdb=" O ARG E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 146 Processing helix chain 'E' and resid 147 through 157 removed outlier: 3.501A pdb=" N LEU E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 186 removed outlier: 3.680A pdb=" N ALA E 177 " --> pdb=" O SER E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 36 removed outlier: 3.587A pdb=" N ALA F 12 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE F 36 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 70 removed outlier: 3.600A pdb=" N PHE F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE F 47 " --> pdb=" O PHE F 43 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE F 52 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 87 Processing helix chain 'F' and resid 90 through 95 Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.564A pdb=" N GLU F 102 " --> pdb=" O PRO F 98 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR F 103 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'F' and resid 133 through 158 removed outlier: 3.546A pdb=" N LEU F 138 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA F 139 " --> pdb=" O PRO F 135 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 143 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU F 155 " --> pdb=" O MET F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 163 removed outlier: 3.550A pdb=" N GLU F 162 " --> pdb=" O TRP F 158 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 163' Processing helix chain 'F' and resid 168 through 180 removed outlier: 3.967A pdb=" N ARG F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'F' and resid 193 through 198 Processing helix chain 'F' and resid 199 through 202 Processing helix chain 'F' and resid 209 through 236 removed outlier: 3.880A pdb=" N TYR F 214 " --> pdb=" O TYR F 210 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 220 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS F 234 " --> pdb=" O LEU F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 266 removed outlier: 3.600A pdb=" N HIS F 249 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 276 removed outlier: 3.520A pdb=" N ILE F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 288 removed outlier: 4.585A pdb=" N HIS F 285 " --> pdb=" O LEU F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 303 removed outlier: 3.946A pdb=" N LEU F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 311 removed outlier: 3.581A pdb=" N LEU F 311 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 343 removed outlier: 3.895A pdb=" N TYR F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL F 337 " --> pdb=" O LEU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 347 Processing helix chain 'F' and resid 357 through 378 removed outlier: 3.586A pdb=" N LEU F 362 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE F 363 " --> pdb=" O LEU F 359 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA2, first strand: chain 'B' and resid 106 through 109 removed outlier: 6.634A pdb=" N LEU B 121 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE B 132 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU B 123 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 170 through 171 Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 226 removed outlier: 7.152A pdb=" N TYR B 225 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL B 198 " --> pdb=" O TYR B 225 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG B 197 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU B 427 " --> pdb=" O MET B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 262 Processing sheet with id=AA7, first strand: chain 'B' and resid 482 through 485 Processing sheet with id=AA8, first strand: chain 'B' and resid 634 through 635 removed outlier: 5.450A pdb=" N ALA B 617 " --> pdb=" O TRP B 649 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU B 581 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL B 661 " --> pdb=" O GLU B 581 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL B 583 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 580 " --> pdb=" O GLY B 695 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY B 695 " --> pdb=" O LEU B 580 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 726 through 727 Processing sheet with id=AB1, first strand: chain 'B' and resid 957 through 961 Processing sheet with id=AB2, first strand: chain 'B' and resid 803 through 805 Processing sheet with id=AB3, first strand: chain 'B' and resid 809 through 810 Processing sheet with id=AB4, first strand: chain 'B' and resid 841 through 843 Processing sheet with id=AB5, first strand: chain 'B' and resid 872 through 873 Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.595A pdb=" N CYS D 162 " --> pdb=" O GLU D 49 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1926 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: 3.67 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.79: 19221 1.79 - 2.40: 150 2.40 - 3.01: 0 3.01 - 3.61: 0 3.61 - 4.22: 3 Bond restraints: 19374 Sorted by residual: bond pdb=" S1 F3S B1106 " pdb="FE4 F3S B1106 " ideal model delta sigma weight residual 2.258 4.221 -1.963 2.00e-02 2.50e+03 9.64e+03 bond pdb=" S4 F3S B1106 " pdb="FE1 F3S B1106 " ideal model delta sigma weight residual 2.233 4.176 -1.943 2.00e-02 2.50e+03 9.44e+03 bond pdb=" S2 F3S B1106 " pdb="FE3 F3S B1106 " ideal model delta sigma weight residual 2.300 4.183 -1.883 2.00e-02 2.50e+03 8.86e+03 bond pdb=" S2 F3S B1106 " pdb="FE4 F3S B1106 " ideal model delta sigma weight residual 2.317 2.197 0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" S3 F3S B1106 " pdb="FE1 F3S B1106 " ideal model delta sigma weight residual 2.296 2.188 0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 19369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.72: 26506 14.72 - 29.45: 11 29.45 - 44.17: 3 44.17 - 58.90: 0 58.90 - 73.62: 2 Bond angle restraints: 26522 Sorted by residual: angle pdb=" S1 F3S B1106 " pdb="FE4 F3S B1106 " pdb=" S3 F3S B1106 " ideal model delta sigma weight residual 114.75 41.13 73.62 3.00e+00 1.11e-01 6.02e+02 angle pdb=" S3 F3S B1106 " pdb="FE1 F3S B1106 " pdb=" S4 F3S B1106 " ideal model delta sigma weight residual 112.59 42.16 70.43 3.00e+00 1.11e-01 5.51e+02 angle pdb=" S1 F3S B1106 " pdb="FE3 F3S B1106 " pdb=" S4 F3S B1106 " ideal model delta sigma weight residual 112.54 144.68 -32.14 3.00e+00 1.11e-01 1.15e+02 angle pdb="FE1 F3S B1106 " pdb=" S4 F3S B1106 " pdb="FE3 F3S B1106 " ideal model delta sigma weight residual 74.86 44.80 30.06 3.00e+00 1.11e-01 1.00e+02 angle pdb=" S2 F3S B1106 " pdb="FE3 F3S B1106 " pdb=" S4 F3S B1106 " ideal model delta sigma weight residual 103.26 73.73 29.53 3.00e+00 1.11e-01 9.69e+01 ... (remaining 26517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 9760 17.48 - 34.96: 1120 34.96 - 52.45: 169 52.45 - 69.93: 40 69.93 - 87.41: 30 Dihedral angle restraints: 11119 sinusoidal: 4399 harmonic: 6720 Sorted by residual: dihedral pdb=" C2B HEC B1101 " pdb=" C3B HEC B1101 " pdb=" CAB HEC B1101 " pdb=" CBB HEC B1101 " ideal model delta sinusoidal sigma weight residual 60.00 146.61 -86.61 2 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" C2B HEC A 302 " pdb=" C3B HEC A 302 " pdb=" CAB HEC A 302 " pdb=" CBB HEC A 302 " ideal model delta sinusoidal sigma weight residual 240.00 173.90 66.10 2 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CA CYS A 224 " pdb=" C CYS A 224 " pdb=" N HIS A 225 " pdb=" CA HIS A 225 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 11116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.961: 2855 2.961 - 5.922: 0 5.922 - 8.883: 0 8.883 - 11.844: 0 11.844 - 14.804: 1 Chirality restraints: 2856 Sorted by residual: chirality pdb=" S2 F3S B1106 " pdb="FE1 F3S B1106 " pdb="FE3 F3S B1106 " pdb="FE4 F3S B1106 " both_signs ideal model delta sigma weight residual False 10.77 -4.04 14.80 2.00e-01 2.50e+01 5.48e+03 chirality pdb=" CA ASN E 132 " pdb=" N ASN E 132 " pdb=" C ASN E 132 " pdb=" CB ASN E 132 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA ARG B 871 " pdb=" N ARG B 871 " pdb=" C ARG B 871 " pdb=" CB ARG B 871 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2853 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC E 202 " 0.013 2.00e-02 2.50e+03 6.57e-02 9.70e+01 pdb=" C2C HEC E 202 " -0.179 2.00e-02 2.50e+03 pdb=" C3C HEC E 202 " 0.022 2.00e-02 2.50e+03 pdb=" C4C HEC E 202 " 0.008 2.00e-02 2.50e+03 pdb=" CAC HEC E 202 " 0.027 2.00e-02 2.50e+03 pdb=" CHC HEC E 202 " 0.030 2.00e-02 2.50e+03 pdb=" CHD HEC E 202 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC E 202 " 0.065 2.00e-02 2.50e+03 pdb=" NC HEC E 202 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 302 " -0.025 2.00e-02 2.50e+03 6.28e-02 8.87e+01 pdb=" C2C HEC A 302 " 0.172 2.00e-02 2.50e+03 pdb=" C3C HEC A 302 " -0.017 2.00e-02 2.50e+03 pdb=" C4C HEC A 302 " -0.006 2.00e-02 2.50e+03 pdb=" CAC HEC A 302 " -0.036 2.00e-02 2.50e+03 pdb=" CHC HEC A 302 " -0.027 2.00e-02 2.50e+03 pdb=" CHD HEC A 302 " 0.005 2.00e-02 2.50e+03 pdb=" CMC HEC A 302 " -0.053 2.00e-02 2.50e+03 pdb=" NC HEC A 302 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 303 " 0.021 2.00e-02 2.50e+03 4.81e-02 5.21e+01 pdb=" C2C HEC A 303 " -0.130 2.00e-02 2.50e+03 pdb=" C3C HEC A 303 " 0.012 2.00e-02 2.50e+03 pdb=" C4C HEC A 303 " 0.001 2.00e-02 2.50e+03 pdb=" CAC HEC A 303 " 0.039 2.00e-02 2.50e+03 pdb=" CHC HEC A 303 " 0.030 2.00e-02 2.50e+03 pdb=" CHD HEC A 303 " -0.007 2.00e-02 2.50e+03 pdb=" CMC HEC A 303 " 0.027 2.00e-02 2.50e+03 pdb=" NC HEC A 303 " 0.006 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 271 2.62 - 3.19: 15568 3.19 - 3.76: 32051 3.76 - 4.33: 46201 4.33 - 4.90: 73684 Nonbonded interactions: 167775 Sorted by model distance: nonbonded pdb=" NE2 HIS A 63 " pdb="FE HEC A 304 " model vdw 2.045 3.080 nonbonded pdb=" NE2 HIS A 66 " pdb="FE HEC A 301 " model vdw 2.073 3.080 nonbonded pdb=" NE2 HIS A 140 " pdb="FE HEC B1101 " model vdw 2.115 3.080 nonbonded pdb=" O THR B 859 " pdb=" OG1 THR B 859 " model vdw 2.184 3.040 nonbonded pdb=" S3 F3S B1106 " pdb="FE3 F3S B1106 " model vdw 2.187 2.688 ... (remaining 167770 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.230 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.027 1.963 19407 Z= 1.325 Angle : 1.514 73.619 26567 Z= 0.620 Chirality : 0.283 14.804 2856 Planarity : 0.008 0.093 3339 Dihedral : 15.530 87.409 6813 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.42 % Allowed : 8.37 % Favored : 91.22 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.59 (0.13), residues: 2317 helix: -4.56 (0.07), residues: 1049 sheet: -3.09 (0.37), residues: 153 loop : -2.83 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 990 TYR 0.026 0.002 TYR E 163 PHE 0.028 0.002 PHE C 266 TRP 0.022 0.002 TRP C 186 HIS 0.007 0.002 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.02513 / 1.24 (19374) covalent geometry : angle 1.33414 / 0.62 (26522) hydrogen bonds : bond 0.28938 / 19.67 ( 677) hydrogen bonds : angle 11.93103 / 8.48 ( 1926) metal coordination : bond 0.32330 / 19.37 ( 15) metal coordination : angle 17.45305 / 12.56 ( 45) Misc. bond : bond 0.13279 / 7.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 436 time to evaluate : 0.608 Fit side-chains REVERT: A 13 ARG cc_start: 0.7598 (tpt90) cc_final: 0.7036 (tpp80) REVERT: B 126 GLU cc_start: 0.7288 (mp0) cc_final: 0.7078 (mp0) REVERT: B 192 GLN cc_start: 0.6941 (mp10) cc_final: 0.6162 (mp10) REVERT: B 313 ARG cc_start: 0.8609 (ptm-80) cc_final: 0.8376 (ptm-80) REVERT: B 694 VAL cc_start: 0.8333 (m) cc_final: 0.8005 (t) REVERT: B 795 LEU cc_start: 0.8563 (mt) cc_final: 0.8031 (mt) REVERT: B 844 ASP cc_start: 0.7775 (m-30) cc_final: 0.7558 (m-30) REVERT: B 968 ARG cc_start: 0.7540 (mtp-110) cc_final: 0.7260 (ttt180) REVERT: C 47 TRP cc_start: 0.7448 (t60) cc_final: 0.7065 (t60) REVERT: C 79 ASN cc_start: 0.8321 (m-40) cc_final: 0.7993 (m110) REVERT: C 207 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7526 (ttmm) REVERT: C 284 LEU cc_start: 0.8591 (tt) cc_final: 0.8348 (tt) REVERT: C 311 MET cc_start: 0.8704 (ttp) cc_final: 0.8489 (ttp) REVERT: E 146 MET cc_start: 0.8403 (ttm) cc_final: 0.8165 (ttm) REVERT: E 153 ASP cc_start: 0.7956 (t70) cc_final: 0.7578 (t0) REVERT: E 157 ASN cc_start: 0.8111 (m110) cc_final: 0.7888 (m-40) REVERT: E 167 TYR cc_start: 0.8484 (p90) cc_final: 0.7995 (p90) REVERT: F 9 LEU cc_start: 0.8410 (tp) cc_final: 0.8205 (tp) REVERT: F 234 LYS cc_start: 0.8281 (tppp) cc_final: 0.8076 (tttp) REVERT: F 319 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7988 (mtt-85) REVERT: F 343 ILE cc_start: 0.8723 (mm) cc_final: 0.8406 (mm) outliers start: 8 outliers final: 4 residues processed: 443 average time/residue: 0.1517 time to fit residues: 100.8310 Evaluate side-chains 330 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 326 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 200] chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN A 87 ASN A 190 ASN A 199 GLN B 138 HIS B 234 ASN B 373 GLN B 378 HIS B 471 HIS B 561 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 GLN B 926 ASN B 955 GLN B 975 GLN C 79 ASN C 141 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN D 174 GLN D 192 ASN E 117 HIS ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 HIS F 304 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.112558 restraints weight = 24976.190| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.44 r_work: 0.3034 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.611 19407 Z= 0.189 Angle : 1.223 64.147 26567 Z= 0.411 Chirality : 0.050 1.369 2856 Planarity : 0.006 0.073 3339 Dihedral : 9.044 86.881 2649 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.66 % Allowed : 12.42 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.99 (0.15), residues: 2317 helix: -2.90 (0.12), residues: 1090 sheet: -2.86 (0.37), residues: 153 loop : -2.20 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 140 TYR 0.019 0.001 TYR F 109 PHE 0.017 0.001 PHE F 167 TRP 0.023 0.001 TRP C 186 HIS 0.005 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (19374) covalent geometry : angle 0.95612 / 0.41 (26522) hydrogen bonds : bond 0.04375 / 2.99 ( 677) hydrogen bonds : angle 6.03972 / 4.30 ( 1926) metal coordination : bond 0.02460 / 1.34 ( 15) metal coordination : angle 18.53976 / 13.18 ( 45) Misc. bond : bond 0.18778 / 11.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 393 time to evaluate : 0.746 Fit side-chains REVERT: A 13 ARG cc_start: 0.7704 (tpt90) cc_final: 0.6901 (tpp80) REVERT: A 53 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7159 (mp0) REVERT: A 186 GLU cc_start: 0.8830 (mp0) cc_final: 0.8592 (mp0) REVERT: A 205 ARG cc_start: 0.8084 (ttp-170) cc_final: 0.7864 (mtp-110) REVERT: B 87 GLU cc_start: 0.7681 (mt-10) cc_final: 0.6515 (mt-10) REVERT: B 126 GLU cc_start: 0.7642 (mp0) cc_final: 0.7394 (mp0) REVERT: B 192 GLN cc_start: 0.7296 (mp10) cc_final: 0.7011 (mp10) REVERT: B 460 TYR cc_start: 0.8819 (m-80) cc_final: 0.8542 (m-80) REVERT: B 597 ASN cc_start: 0.9120 (t0) cc_final: 0.8470 (t0) REVERT: B 694 VAL cc_start: 0.8387 (m) cc_final: 0.7909 (t) REVERT: B 721 LYS cc_start: 0.7021 (mmmt) cc_final: 0.6791 (mmmt) REVERT: B 844 ASP cc_start: 0.8150 (m-30) cc_final: 0.7877 (m-30) REVERT: B 920 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8943 (m-10) REVERT: B 968 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7550 (ttt180) REVERT: C 14 MET cc_start: 0.7541 (ttt) cc_final: 0.7178 (tpt) REVERT: C 30 ARG cc_start: 0.7342 (ttp80) cc_final: 0.7080 (ttp80) REVERT: C 35 ILE cc_start: 0.8127 (mt) cc_final: 0.7853 (mp) REVERT: C 113 GLN cc_start: 0.7880 (mt0) cc_final: 0.7617 (mt0) REVERT: C 157 THR cc_start: 0.8852 (p) cc_final: 0.8646 (p) REVERT: C 311 MET cc_start: 0.8933 (ttp) cc_final: 0.8647 (ttp) REVERT: D 49 GLU cc_start: 0.8040 (mp0) cc_final: 0.6964 (mm-30) REVERT: E 37 MET cc_start: 0.9195 (mtm) cc_final: 0.8973 (mtm) REVERT: E 110 ARG cc_start: 0.8360 (ttm110) cc_final: 0.7698 (mtm-85) REVERT: E 157 ASN cc_start: 0.8431 (m110) cc_final: 0.8047 (m-40) REVERT: E 167 TYR cc_start: 0.8799 (p90) cc_final: 0.7879 (p90) REVERT: F 131 TYR cc_start: 0.9035 (t80) cc_final: 0.8776 (t80) REVERT: F 179 SER cc_start: 0.8712 (p) cc_final: 0.8453 (t) REVERT: F 209 MET cc_start: 0.8033 (tpp) cc_final: 0.7783 (ttt) REVERT: F 383 LEU cc_start: 0.7382 (tp) cc_final: 0.7163 (tp) outliers start: 32 outliers final: 22 residues processed: 417 average time/residue: 0.1461 time to fit residues: 92.1756 Evaluate side-chains 368 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 345 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: [185, 212, 48, 6, 211, 121, 142, 207, 158, 118, 136] chunk 185 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 0.2980 chunk 211 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 390 ASN B 854 ASN B 936 ASN C 79 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN F 41 GLN F 44 HIS F 353 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.139500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.114782 restraints weight = 24934.720| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.51 r_work: 0.3041 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.562 19407 Z= 0.142 Angle : 1.110 83.108 26567 Z= 0.370 Chirality : 0.052 1.522 2856 Planarity : 0.005 0.069 3339 Dihedral : 8.611 86.024 2649 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.34 % Allowed : 13.15 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.16), residues: 2317 helix: -1.84 (0.14), residues: 1087 sheet: -2.71 (0.39), residues: 145 loop : -1.91 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 222 TYR 0.027 0.001 TYR F 109 PHE 0.014 0.001 PHE C 279 TRP 0.027 0.001 TRP C 186 HIS 0.005 0.001 HIS B 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (19374) covalent geometry : angle 0.85865 / 0.37 (26522) hydrogen bonds : bond 0.03811 / 2.60 ( 677) hydrogen bonds : angle 5.25347 / 3.75 ( 1926) metal coordination : bond 0.00931 / 0.52 ( 15) metal coordination : angle 17.11401 / 11.38 ( 45) Misc. bond : bond 0.17808 / 11.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 360 time to evaluate : 0.632 Fit side-chains REVERT: A 40 LEU cc_start: 0.8942 (tp) cc_final: 0.8706 (tp) REVERT: A 186 GLU cc_start: 0.8848 (mp0) cc_final: 0.8617 (mp0) REVERT: A 205 ARG cc_start: 0.8077 (ttp-170) cc_final: 0.7862 (mtp-110) REVERT: B 87 GLU cc_start: 0.7667 (mt-10) cc_final: 0.6163 (mt-10) REVERT: B 158 ASP cc_start: 0.8889 (t0) cc_final: 0.7807 (t0) REVERT: B 192 GLN cc_start: 0.7285 (mp10) cc_final: 0.7076 (mp10) REVERT: B 276 MET cc_start: 0.9254 (mmm) cc_final: 0.8950 (mtp) REVERT: B 313 ARG cc_start: 0.8517 (ptm-80) cc_final: 0.8248 (ptm-80) REVERT: B 597 ASN cc_start: 0.9185 (t0) cc_final: 0.8334 (t0) REVERT: B 694 VAL cc_start: 0.8344 (m) cc_final: 0.7808 (t) REVERT: B 721 LYS cc_start: 0.7046 (mmmt) cc_final: 0.6822 (mmmm) REVERT: B 844 ASP cc_start: 0.8085 (m-30) cc_final: 0.7812 (m-30) REVERT: B 851 MET cc_start: 0.9147 (tpt) cc_final: 0.8541 (tpt) REVERT: B 920 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8868 (m-10) REVERT: B 968 ARG cc_start: 0.7853 (mtp-110) cc_final: 0.7516 (ttt180) REVERT: C 14 MET cc_start: 0.7467 (ttt) cc_final: 0.7182 (tpt) REVERT: C 113 GLN cc_start: 0.7855 (mt0) cc_final: 0.7624 (mt0) REVERT: C 157 THR cc_start: 0.8761 (p) cc_final: 0.8545 (p) REVERT: C 193 ASP cc_start: 0.8353 (t70) cc_final: 0.8147 (t70) REVERT: C 200 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7043 (mmm-85) REVERT: C 311 MET cc_start: 0.8959 (ttp) cc_final: 0.8729 (ttp) REVERT: D 34 LEU cc_start: 0.7782 (pp) cc_final: 0.7160 (tt) REVERT: D 49 GLU cc_start: 0.8077 (mp0) cc_final: 0.7104 (mm-30) REVERT: E 96 ARG cc_start: 0.7311 (mmt90) cc_final: 0.6993 (mmt-90) REVERT: E 117 HIS cc_start: 0.8933 (OUTLIER) cc_final: 0.7577 (m90) REVERT: E 146 MET cc_start: 0.8603 (ttm) cc_final: 0.8364 (ttm) REVERT: E 157 ASN cc_start: 0.8456 (m110) cc_final: 0.8023 (m-40) REVERT: E 167 TYR cc_start: 0.8711 (p90) cc_final: 0.7737 (p90) REVERT: F 28 MET cc_start: 0.6719 (tpt) cc_final: 0.6506 (tpt) REVERT: F 131 TYR cc_start: 0.8983 (t80) cc_final: 0.8623 (t80) REVERT: F 383 LEU cc_start: 0.7364 (tp) cc_final: 0.7071 (tp) outliers start: 45 outliers final: 27 residues processed: 394 average time/residue: 0.1437 time to fit residues: 87.2488 Evaluate side-chains 357 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 328 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: [104, 138, 136, 77, 8, 66, 70, 155, 162, 58, 114] chunk 104 optimal weight: 7.9990 chunk 138 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 77 optimal weight: 0.0170 chunk 8 optimal weight: 20.0000 chunk 66 optimal weight: 0.0050 chunk 70 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 overall best weight: 0.4434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 602 GLN C 79 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.140586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.116575 restraints weight = 24880.787| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.40 r_work: 0.3147 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.493 19407 Z= 0.128 Angle : 1.079 83.721 26567 Z= 0.358 Chirality : 0.050 1.424 2856 Planarity : 0.005 0.064 3339 Dihedral : 8.228 86.887 2649 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.34 % Allowed : 14.86 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.17), residues: 2317 helix: -1.18 (0.15), residues: 1083 sheet: -2.57 (0.39), residues: 154 loop : -1.74 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 70 TYR 0.030 0.001 TYR E 152 PHE 0.012 0.001 PHE F 167 TRP 0.020 0.001 TRP C 186 HIS 0.008 0.001 HIS B 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (19374) covalent geometry : angle 0.83617 / 0.35 (26522) hydrogen bonds : bond 0.03442 / 2.36 ( 677) hydrogen bonds : angle 4.88662 / 3.51 ( 1926) metal coordination : bond 0.00612 / 0.31 ( 15) metal coordination : angle 16.59280 / 11.19 ( 45) Misc. bond : bond 0.13820 / 7.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 379 time to evaluate : 0.722 Fit side-chains REVERT: A 186 GLU cc_start: 0.8761 (mp0) cc_final: 0.8529 (mp0) REVERT: A 205 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7819 (mtp-110) REVERT: B 87 GLU cc_start: 0.7508 (mt-10) cc_final: 0.5907 (mt-10) REVERT: B 158 ASP cc_start: 0.8701 (t0) cc_final: 0.7910 (t0) REVERT: B 225 TYR cc_start: 0.7822 (m-80) cc_final: 0.7542 (m-80) REVERT: B 252 ARG cc_start: 0.7536 (ttm170) cc_final: 0.7215 (ttm170) REVERT: B 276 MET cc_start: 0.9126 (mmm) cc_final: 0.8839 (mtp) REVERT: B 313 ARG cc_start: 0.8393 (ptm-80) cc_final: 0.8106 (ptm-80) REVERT: B 418 GLU cc_start: 0.7438 (tp30) cc_final: 0.7214 (tp30) REVERT: B 597 ASN cc_start: 0.9090 (t0) cc_final: 0.8655 (t0) REVERT: B 603 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8083 (mm-30) REVERT: B 694 VAL cc_start: 0.8317 (m) cc_final: 0.7813 (t) REVERT: B 721 LYS cc_start: 0.6961 (mmmt) cc_final: 0.6755 (mmmm) REVERT: B 808 TYR cc_start: 0.8837 (m-80) cc_final: 0.8447 (m-80) REVERT: B 851 MET cc_start: 0.9136 (tpt) cc_final: 0.8629 (tpt) REVERT: B 920 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8907 (m-10) REVERT: B 968 ARG cc_start: 0.7812 (mtp-110) cc_final: 0.7507 (ttt180) REVERT: C 157 THR cc_start: 0.8698 (p) cc_final: 0.8454 (p) REVERT: C 200 ARG cc_start: 0.7595 (mmm160) cc_final: 0.6895 (mmm-85) REVERT: C 207 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7164 (ttmm) REVERT: C 311 MET cc_start: 0.8946 (ttp) cc_final: 0.8728 (ttp) REVERT: D 34 LEU cc_start: 0.7613 (pp) cc_final: 0.7121 (tt) REVERT: D 150 ASN cc_start: 0.6847 (p0) cc_final: 0.6625 (p0) REVERT: E 96 ARG cc_start: 0.7193 (mmt90) cc_final: 0.6882 (mmt-90) REVERT: E 110 ARG cc_start: 0.8381 (ttm110) cc_final: 0.7707 (mtm-85) REVERT: E 146 MET cc_start: 0.8391 (ttm) cc_final: 0.8112 (ttm) REVERT: E 157 ASN cc_start: 0.8385 (m110) cc_final: 0.8002 (m-40) REVERT: E 167 TYR cc_start: 0.8780 (p90) cc_final: 0.7815 (p90) REVERT: F 131 TYR cc_start: 0.8976 (t80) cc_final: 0.8518 (t80) REVERT: F 192 PHE cc_start: 0.8581 (m-10) cc_final: 0.8227 (m-80) REVERT: F 234 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7155 (tmtt) REVERT: F 332 TYR cc_start: 0.8055 (m-10) cc_final: 0.7421 (m-10) REVERT: F 383 LEU cc_start: 0.7368 (tp) cc_final: 0.7125 (tp) outliers start: 45 outliers final: 28 residues processed: 412 average time/residue: 0.1381 time to fit residues: 87.5321 Evaluate side-chains 369 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 340 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: [3, 104, 155, 60, 114, 38, 146, 160, 194, 22, 26] chunk 3 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN B 387 GLN B 390 ASN B 800 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.133124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107831 restraints weight = 25016.772| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.44 r_work: 0.3172 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.587 19407 Z= 0.202 Angle : 1.112 84.019 26567 Z= 0.382 Chirality : 0.053 1.451 2856 Planarity : 0.005 0.067 3339 Dihedral : 8.303 87.942 2649 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.44 % Allowed : 16.42 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.17), residues: 2317 helix: -1.03 (0.15), residues: 1094 sheet: -2.49 (0.40), residues: 158 loop : -1.67 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 871 TYR 0.020 0.002 TYR C 269 PHE 0.033 0.002 PHE F 136 TRP 0.021 0.001 TRP F 53 HIS 0.010 0.001 HIS B 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (19374) covalent geometry : angle 0.88754 / 0.38 (26522) hydrogen bonds : bond 0.03707 / 2.53 ( 677) hydrogen bonds : angle 4.83397 / 3.46 ( 1926) metal coordination : bond 0.01404 / 0.81 ( 15) metal coordination : angle 16.30725 / 10.67 ( 45) Misc. bond : bond 0.18401 / 10.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 350 time to evaluate : 0.540 Fit side-chains REVERT: A 186 GLU cc_start: 0.8860 (mp0) cc_final: 0.8647 (mp0) REVERT: A 205 ARG cc_start: 0.8178 (ttp-170) cc_final: 0.7949 (mtp-110) REVERT: B 87 GLU cc_start: 0.7773 (mt-10) cc_final: 0.6065 (mt-10) REVERT: B 158 ASP cc_start: 0.8862 (t0) cc_final: 0.8412 (t0) REVERT: B 418 GLU cc_start: 0.7615 (tp30) cc_final: 0.7406 (tp30) REVERT: B 694 VAL cc_start: 0.8398 (m) cc_final: 0.7923 (t) REVERT: B 721 LYS cc_start: 0.7131 (mmmt) cc_final: 0.6871 (mmmm) REVERT: B 799 MET cc_start: 0.8467 (mmm) cc_final: 0.8217 (mmm) REVERT: B 820 MET cc_start: 0.8591 (ttt) cc_final: 0.8264 (ttp) REVERT: B 865 ASN cc_start: 0.8532 (t0) cc_final: 0.8255 (t0) REVERT: B 916 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7973 (mt-10) REVERT: B 918 CYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8301 (t) REVERT: B 968 ARG cc_start: 0.8096 (mtp-110) cc_final: 0.7747 (ttt180) REVERT: C 193 ASP cc_start: 0.8305 (t0) cc_final: 0.8102 (t0) REVERT: C 207 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7572 (ttmm) REVERT: C 279 PHE cc_start: 0.8759 (m-80) cc_final: 0.8519 (m-80) REVERT: C 370 LYS cc_start: 0.8435 (tttp) cc_final: 0.7972 (mttt) REVERT: D 34 LEU cc_start: 0.7829 (pp) cc_final: 0.7393 (tt) REVERT: D 49 GLU cc_start: 0.8148 (mp0) cc_final: 0.7113 (mm-30) REVERT: D 160 PHE cc_start: 0.8145 (m-80) cc_final: 0.7868 (m-80) REVERT: D 173 LYS cc_start: 0.6599 (mppt) cc_final: 0.6225 (tmtt) REVERT: E 96 ARG cc_start: 0.7218 (mmt90) cc_final: 0.6916 (mmt-90) REVERT: E 146 MET cc_start: 0.8375 (ttm) cc_final: 0.8082 (ttm) REVERT: E 157 ASN cc_start: 0.8590 (m110) cc_final: 0.8236 (m-40) REVERT: E 167 TYR cc_start: 0.8989 (p90) cc_final: 0.8071 (p90) REVERT: F 131 TYR cc_start: 0.9049 (t80) cc_final: 0.8682 (t80) REVERT: F 192 PHE cc_start: 0.8603 (m-10) cc_final: 0.8391 (m-80) REVERT: F 234 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7463 (tmtt) REVERT: F 282 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8841 (p) REVERT: F 332 TYR cc_start: 0.8333 (m-10) cc_final: 0.7555 (m-80) REVERT: F 383 LEU cc_start: 0.7287 (tp) cc_final: 0.7027 (tp) outliers start: 47 outliers final: 38 residues processed: 378 average time/residue: 0.1363 time to fit residues: 80.0295 Evaluate side-chains 367 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 327 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: [32, 2, 169, 62, 159, 182, 139, 166, 184, 37, 90] chunk 32 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 166 optimal weight: 0.5980 chunk 184 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 HIS F 348 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.130459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.105053 restraints weight = 24904.910| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.47 r_work: 0.2944 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.608 19407 Z= 0.224 Angle : 1.124 83.699 26567 Z= 0.389 Chirality : 0.054 1.482 2856 Planarity : 0.005 0.069 3339 Dihedral : 8.289 86.829 2649 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.91 % Allowed : 17.05 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.17), residues: 2317 helix: -0.90 (0.15), residues: 1095 sheet: -2.54 (0.42), residues: 146 loop : -1.70 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 558 TYR 0.021 0.002 TYR C 269 PHE 0.017 0.002 PHE C 279 TRP 0.020 0.001 TRP F 53 HIS 0.007 0.001 HIS B 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (19374) covalent geometry : angle 0.90020 / 0.39 (26522) hydrogen bonds : bond 0.03800 / 2.59 ( 677) hydrogen bonds : angle 4.87192 / 3.50 ( 1926) metal coordination : bond 0.01578 / 0.90 ( 15) metal coordination : angle 16.37919 / 10.67 ( 45) Misc. bond : bond 0.19956 / 11.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 331 time to evaluate : 0.676 Fit side-chains REVERT: A 186 GLU cc_start: 0.8802 (mp0) cc_final: 0.8547 (mp0) REVERT: B 87 GLU cc_start: 0.7752 (mt-10) cc_final: 0.6150 (mt-10) REVERT: B 313 ARG cc_start: 0.8829 (ptm-80) cc_final: 0.8610 (ptm-80) REVERT: B 418 GLU cc_start: 0.7646 (tp30) cc_final: 0.7404 (tp30) REVERT: B 683 ARG cc_start: 0.8541 (mmt180) cc_final: 0.8339 (mmt180) REVERT: B 694 VAL cc_start: 0.8369 (m) cc_final: 0.7889 (t) REVERT: B 820 MET cc_start: 0.8721 (ttt) cc_final: 0.8328 (ttp) REVERT: B 865 ASN cc_start: 0.8628 (t0) cc_final: 0.8347 (t0) REVERT: B 918 CYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8391 (t) REVERT: B 968 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7516 (ttt180) REVERT: C 207 LYS cc_start: 0.7579 (ttmt) cc_final: 0.7133 (ttmm) REVERT: C 370 LYS cc_start: 0.8310 (tttp) cc_final: 0.7759 (mtmm) REVERT: D 34 LEU cc_start: 0.7809 (pp) cc_final: 0.7283 (tt) REVERT: D 49 GLU cc_start: 0.8214 (mp0) cc_final: 0.7067 (mm-30) REVERT: D 173 LYS cc_start: 0.6647 (mppt) cc_final: 0.6257 (tmtt) REVERT: E 157 ASN cc_start: 0.8645 (m110) cc_final: 0.8220 (m-40) REVERT: E 167 TYR cc_start: 0.8966 (p90) cc_final: 0.8081 (p90) REVERT: F 9 LEU cc_start: 0.8510 (tp) cc_final: 0.8195 (tp) REVERT: F 54 MET cc_start: 0.8298 (tpp) cc_final: 0.8063 (tpp) REVERT: F 131 TYR cc_start: 0.9113 (t80) cc_final: 0.8782 (t80) REVERT: F 192 PHE cc_start: 0.8731 (m-10) cc_final: 0.8490 (m-80) REVERT: F 234 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7498 (tmtt) REVERT: F 318 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8752 (ttpt) REVERT: F 332 TYR cc_start: 0.8300 (m-10) cc_final: 0.7508 (m-80) REVERT: F 383 LEU cc_start: 0.7270 (tp) cc_final: 0.6970 (tp) outliers start: 56 outliers final: 44 residues processed: 370 average time/residue: 0.1397 time to fit residues: 79.3111 Evaluate side-chains 355 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 310 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: [38, 127, 116, 20, 9, 157, 192, 205, 84, 215, 209] chunk 38 optimal weight: 8.9990 chunk 127 optimal weight: 0.2980 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 30.0000 chunk 157 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 209 optimal weight: 0.3980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 874 ASN C 23 GLN ** C 163 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 = 0.3428 r_free = 0.3428 target = 0.133762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.108550 restraints weight = 24899.651| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.52 r_work: 0.3019 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.571 19407 Z= 0.164 Angle : 1.082 83.468 26567 Z= 0.370 Chirality : 0.052 1.484 2856 Planarity : 0.005 0.066 3339 Dihedral : 8.147 86.122 2649 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.86 % Allowed : 17.41 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.18), residues: 2317 helix: -0.68 (0.16), residues: 1093 sheet: -2.53 (0.39), residues: 167 loop : -1.55 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 320 TYR 0.045 0.001 TYR F 109 PHE 0.016 0.001 PHE C 279 TRP 0.019 0.001 TRP F 53 HIS 0.006 0.001 HIS B 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (19374) covalent geometry : angle 0.86367 / 0.37 (26522) hydrogen bonds : bond 0.03546 / 2.43 ( 677) hydrogen bonds : angle 4.77459 / 3.43 ( 1926) metal coordination : bond 0.00916 / 0.46 ( 15) metal coordination : angle 15.84135 / 10.35 ( 45) Misc. bond : bond 0.18047 / 10.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 341 time to evaluate : 0.559 Fit side-chains REVERT: A 13 ARG cc_start: 0.7740 (tpt-90) cc_final: 0.6929 (tpp80) REVERT: A 186 GLU cc_start: 0.8795 (mp0) cc_final: 0.8534 (mp0) REVERT: B 87 GLU cc_start: 0.7621 (mt-10) cc_final: 0.5993 (mt-10) REVERT: B 313 ARG cc_start: 0.8735 (ptm-80) cc_final: 0.8514 (ptm-80) REVERT: B 418 GLU cc_start: 0.7606 (tp30) cc_final: 0.7361 (tp30) REVERT: B 603 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8207 (mm-30) REVERT: B 683 ARG cc_start: 0.8482 (mmt180) cc_final: 0.8211 (mmt180) REVERT: B 694 VAL cc_start: 0.8496 (m) cc_final: 0.7978 (t) REVERT: B 820 MET cc_start: 0.8671 (ttt) cc_final: 0.8259 (ttp) REVERT: B 865 ASN cc_start: 0.8592 (t0) cc_final: 0.8292 (t0) REVERT: B 918 CYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8376 (t) REVERT: B 968 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7537 (ttt180) REVERT: C 207 LYS cc_start: 0.7458 (ttmt) cc_final: 0.7008 (ttmm) REVERT: C 370 LYS cc_start: 0.8240 (tttp) cc_final: 0.7666 (mttt) REVERT: D 34 LEU cc_start: 0.7750 (pp) cc_final: 0.7262 (tt) REVERT: D 59 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7394 (tt) REVERT: D 173 LYS cc_start: 0.6516 (mppt) cc_final: 0.6167 (tmtt) REVERT: E 152 TYR cc_start: 0.8670 (t80) cc_final: 0.8372 (t80) REVERT: E 157 ASN cc_start: 0.8574 (m110) cc_final: 0.8125 (m-40) REVERT: E 167 TYR cc_start: 0.8876 (p90) cc_final: 0.7881 (p90) REVERT: F 9 LEU cc_start: 0.8487 (tp) cc_final: 0.8182 (tp) REVERT: F 131 TYR cc_start: 0.9065 (t80) cc_final: 0.8768 (t80) REVERT: F 192 PHE cc_start: 0.8672 (m-10) cc_final: 0.8304 (m-80) REVERT: F 234 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7429 (tmtt) REVERT: F 318 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8698 (ttpt) REVERT: F 332 TYR cc_start: 0.8190 (m-10) cc_final: 0.7397 (m-10) REVERT: F 383 LEU cc_start: 0.7269 (tp) cc_final: 0.7013 (tp) outliers start: 55 outliers final: 40 residues processed: 376 average time/residue: 0.1346 time to fit residues: 78.5685 Evaluate side-chains 363 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 321 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 353 HIS Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: [110, 213, 24, 166, 132, 77, 191, 102, 44, 67, 181] chunk 110 optimal weight: 0.9990 chunk 213 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 chunk 166 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 191 optimal weight: 6.9990 chunk 102 optimal weight: 0.0570 chunk 44 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 181 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 390 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 HIS F 396 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.139556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.115996 restraints weight = 24752.687| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.34 r_work: 0.3186 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.479 19407 Z= 0.131 Angle : 1.045 83.067 26567 Z= 0.358 Chirality : 0.051 1.496 2856 Planarity : 0.005 0.065 3339 Dihedral : 7.843 86.612 2649 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.92 % Allowed : 19.18 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 2317 helix: -0.37 (0.16), residues: 1101 sheet: -2.43 (0.39), residues: 166 loop : -1.48 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 558 TYR 0.038 0.001 TYR F 109 PHE 0.012 0.001 PHE F 267 TRP 0.017 0.001 TRP F 53 HIS 0.005 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (19374) covalent geometry : angle 0.83945 / 0.35 (26522) hydrogen bonds : bond 0.03283 / 2.27 ( 677) hydrogen bonds : angle 4.62365 / 3.31 ( 1926) metal coordination : bond 0.00461 / 0.23 ( 15) metal coordination : angle 15.15044 / 9.98 ( 45) Misc. bond : bond 0.13173 / 7.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 361 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7652 (tpt-90) cc_final: 0.6838 (tpp80) REVERT: A 116 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8495 (mt-10) REVERT: A 205 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7885 (mtp-110) REVERT: B 87 GLU cc_start: 0.7351 (mt-10) cc_final: 0.5764 (mt-10) REVERT: B 418 GLU cc_start: 0.7448 (tp30) cc_final: 0.7214 (tp30) REVERT: B 603 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 683 ARG cc_start: 0.8360 (mmt180) cc_final: 0.8021 (mmt180) REVERT: B 694 VAL cc_start: 0.8451 (m) cc_final: 0.7975 (t) REVERT: B 703 GLU cc_start: 0.7480 (tp30) cc_final: 0.7269 (tp30) REVERT: B 704 ASN cc_start: 0.8361 (m-40) cc_final: 0.7630 (t0) REVERT: B 820 MET cc_start: 0.8268 (ttt) cc_final: 0.7815 (ttp) REVERT: B 920 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8857 (m-10) REVERT: B 968 ARG cc_start: 0.7861 (mtp-110) cc_final: 0.7497 (ttt180) REVERT: C 17 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6950 (mm-30) REVERT: C 193 ASP cc_start: 0.8230 (t0) cc_final: 0.7949 (t0) REVERT: C 200 ARG cc_start: 0.7541 (mmm160) cc_final: 0.6873 (mmm-85) REVERT: C 207 LYS cc_start: 0.7653 (ttmt) cc_final: 0.7224 (ttmm) REVERT: C 370 LYS cc_start: 0.8359 (tttp) cc_final: 0.7692 (mttt) REVERT: D 49 GLU cc_start: 0.7791 (mp0) cc_final: 0.6960 (mm-30) REVERT: D 142 TYR cc_start: 0.7258 (t80) cc_final: 0.7030 (t80) REVERT: E 96 ARG cc_start: 0.7179 (mmt90) cc_final: 0.6881 (mmt-90) REVERT: E 152 TYR cc_start: 0.8557 (t80) cc_final: 0.8357 (t80) REVERT: E 157 ASN cc_start: 0.8453 (m110) cc_final: 0.7977 (m-40) REVERT: E 167 TYR cc_start: 0.8754 (p90) cc_final: 0.7820 (p90) REVERT: F 9 LEU cc_start: 0.8445 (tp) cc_final: 0.8148 (tp) REVERT: F 96 PHE cc_start: 0.8371 (t80) cc_final: 0.8056 (t80) REVERT: F 107 THR cc_start: 0.8527 (p) cc_final: 0.8313 (t) REVERT: F 192 PHE cc_start: 0.8494 (m-10) cc_final: 0.8179 (m-80) REVERT: F 234 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7309 (tmtt) REVERT: F 318 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8585 (ttpt) REVERT: F 332 TYR cc_start: 0.8017 (m-10) cc_final: 0.7358 (m-10) REVERT: F 343 ILE cc_start: 0.8879 (mm) cc_final: 0.8574 (mm) outliers start: 37 outliers final: 25 residues processed: 382 average time/residue: 0.1359 time to fit residues: 80.8285 Evaluate side-chains 362 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 336 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: [68, 25, 62, 212, 180, 110, 98, 34, 61, 209, 131] chunk 68 optimal weight: 0.0070 chunk 25 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 209 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 79 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS F 355 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.144669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121199 restraints weight = 23941.526| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.31 r_work: 0.3265 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.530 19407 Z= 0.168 Angle : 1.063 83.115 26567 Z= 0.370 Chirality : 0.053 1.490 2856 Planarity : 0.005 0.066 3339 Dihedral : 7.861 88.151 2649 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.03 % Allowed : 19.18 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.18), residues: 2317 helix: -0.24 (0.16), residues: 1089 sheet: -2.32 (0.40), residues: 168 loop : -1.45 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 558 TYR 0.038 0.002 TYR F 109 PHE 0.017 0.001 PHE C 279 TRP 0.019 0.001 TRP F 53 HIS 0.006 0.001 HIS B 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.16 (19374) covalent geometry : angle 0.86486 / 0.37 (26522) hydrogen bonds : bond 0.03437 / 2.35 ( 677) hydrogen bonds : angle 4.61749 / 3.32 ( 1926) metal coordination : bond 0.00945 / 0.54 ( 15) metal coordination : angle 15.05213 / 9.75 ( 45) Misc. bond : bond 0.17002 / 10.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 339 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7746 (tpt-90) cc_final: 0.7006 (tpp80) REVERT: B 87 GLU cc_start: 0.7470 (mt-10) cc_final: 0.5913 (mt-10) REVERT: B 276 MET cc_start: 0.9099 (mmm) cc_final: 0.8795 (mtp) REVERT: B 418 GLU cc_start: 0.7459 (tp30) cc_final: 0.7226 (tp30) REVERT: B 603 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8018 (mm-30) REVERT: B 683 ARG cc_start: 0.8510 (mmt180) cc_final: 0.8174 (mmt180) REVERT: B 694 VAL cc_start: 0.8461 (m) cc_final: 0.8002 (t) REVERT: B 704 ASN cc_start: 0.8361 (m-40) cc_final: 0.7811 (t0) REVERT: B 918 CYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8246 (t) REVERT: B 920 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8796 (m-10) REVERT: B 968 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7647 (ttt180) REVERT: C 17 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6988 (mm-30) REVERT: C 59 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8170 (tp) REVERT: C 193 ASP cc_start: 0.8334 (t0) cc_final: 0.8059 (t0) REVERT: C 200 ARG cc_start: 0.7629 (mmm160) cc_final: 0.6984 (mmm-85) REVERT: C 207 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7409 (ttmm) REVERT: C 370 LYS cc_start: 0.8491 (tttp) cc_final: 0.7984 (mtmm) REVERT: D 49 GLU cc_start: 0.7877 (mp0) cc_final: 0.7126 (mm-30) REVERT: D 142 TYR cc_start: 0.7398 (t80) cc_final: 0.7193 (t80) REVERT: E 96 ARG cc_start: 0.7169 (mmt90) cc_final: 0.6890 (mmt-90) REVERT: E 152 TYR cc_start: 0.8609 (t80) cc_final: 0.8390 (t80) REVERT: E 157 ASN cc_start: 0.8505 (m110) cc_final: 0.8062 (m-40) REVERT: E 167 TYR cc_start: 0.8868 (p90) cc_final: 0.7979 (p90) REVERT: F 151 MET cc_start: 0.8332 (ttp) cc_final: 0.8110 (ttm) REVERT: F 234 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7394 (tmtt) REVERT: F 332 TYR cc_start: 0.8156 (m-10) cc_final: 0.7352 (m-10) outliers start: 39 outliers final: 30 residues processed: 363 average time/residue: 0.1407 time to fit residues: 78.6909 Evaluate side-chains 362 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 329 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 799 MET Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: [89, 129, 211, 102, 35, 37, 137, 181, 199, 106, 70] chunk 89 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 473 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.135831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.112924 restraints weight = 24696.275| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.25 r_work: 0.3053 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.531 19407 Z= 0.168 Angle : 1.067 82.801 26567 Z= 0.373 Chirality : 0.053 1.522 2856 Planarity : 0.005 0.066 3339 Dihedral : 7.829 88.165 2649 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.77 % Allowed : 19.49 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.18), residues: 2317 helix: -0.19 (0.16), residues: 1096 sheet: -2.33 (0.39), residues: 169 loop : -1.42 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 205 TYR 0.038 0.002 TYR F 109 PHE 0.018 0.001 PHE C 279 TRP 0.018 0.001 TRP F 53 HIS 0.006 0.001 HIS B 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (19374) covalent geometry : angle 0.87020 / 0.37 (26522) hydrogen bonds : bond 0.03452 / 2.36 ( 677) hydrogen bonds : angle 4.62016 / 3.32 ( 1926) metal coordination : bond 0.00924 / 0.49 ( 15) metal coordination : angle 15.02678 / 9.71 ( 45) Misc. bond : bond 0.16502 / 9.84 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 324 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7699 (tpt-90) cc_final: 0.6911 (tpp80) REVERT: A 191 MET cc_start: 0.8777 (mmm) cc_final: 0.8486 (mmp) REVERT: A 205 ARG cc_start: 0.8235 (mtp-110) cc_final: 0.7927 (mtm110) REVERT: B 87 GLU cc_start: 0.7367 (mt-10) cc_final: 0.5814 (mt-10) REVERT: B 418 GLU cc_start: 0.7425 (tp30) cc_final: 0.7187 (tp30) REVERT: B 603 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8103 (mm-30) REVERT: B 683 ARG cc_start: 0.8472 (mmt180) cc_final: 0.8099 (mmt180) REVERT: B 694 VAL cc_start: 0.8460 (m) cc_final: 0.7977 (t) REVERT: B 704 ASN cc_start: 0.8356 (m-40) cc_final: 0.7728 (t0) REVERT: B 918 CYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8267 (t) REVERT: B 920 PHE cc_start: 0.9335 (OUTLIER) cc_final: 0.8824 (m-10) REVERT: B 968 ARG cc_start: 0.7840 (mtp-110) cc_final: 0.7478 (ttt180) REVERT: C 17 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6964 (mm-30) REVERT: C 59 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8199 (tp) REVERT: C 193 ASP cc_start: 0.8340 (t0) cc_final: 0.8028 (t0) REVERT: C 200 ARG cc_start: 0.7588 (mmm160) cc_final: 0.6932 (mmm-85) REVERT: C 207 LYS cc_start: 0.7517 (ttmt) cc_final: 0.7081 (ttmm) REVERT: C 370 LYS cc_start: 0.8433 (tttp) cc_final: 0.7838 (mtmm) REVERT: D 49 GLU cc_start: 0.7968 (mp0) cc_final: 0.7038 (mm-30) REVERT: D 142 TYR cc_start: 0.7325 (t80) cc_final: 0.7103 (t80) REVERT: E 96 ARG cc_start: 0.7190 (mmt90) cc_final: 0.6887 (mmt-90) REVERT: E 157 ASN cc_start: 0.8505 (m110) cc_final: 0.8052 (m-40) REVERT: E 167 TYR cc_start: 0.8861 (p90) cc_final: 0.7946 (p90) REVERT: F 234 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7359 (tmtt) REVERT: F 318 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8705 (ttpt) REVERT: F 332 TYR cc_start: 0.8129 (m-10) cc_final: 0.7408 (m-10) outliers start: 34 outliers final: 31 residues processed: 346 average time/residue: 0.1403 time to fit residues: 74.9293 Evaluate side-chains 364 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 330 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 799 MET Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: [31, 97, 208, 144, 51, 65, 59, 48, 57, 213, 96] chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 0.0020 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 213 optimal weight: 0.2980 chunk 96 optimal weight: 3.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 936 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.137979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.115197 restraints weight = 24635.543| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.26 r_work: 0.3095 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.482 19407 Z= 0.145 Angle : 1.044 82.426 26567 Z= 0.365 Chirality : 0.052 1.534 2856 Planarity : 0.005 0.065 3339 Dihedral : 7.680 88.636 2649 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.92 % Allowed : 19.28 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.18), residues: 2317 helix: -0.04 (0.16), residues: 1093 sheet: -2.25 (0.40), residues: 168 loop : -1.38 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.026 0.001 TYR E 152 PHE 0.016 0.001 PHE C 279 TRP 0.016 0.001 TRP F 190 HIS 0.006 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (19374) covalent geometry : angle 0.85535 / 0.36 (26522) hydrogen bonds : bond 0.03346 / 2.30 ( 677) hydrogen bonds : angle 4.58759 / 3.30 ( 1926) metal coordination : bond 0.00648 / 0.31 ( 15) metal coordination : angle 14.57202 / 9.42 ( 45) Misc. bond : bond 0.14500 / 8.55 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4766.78 seconds wall clock time: 82 minutes 15.32 seconds (4935.32 seconds total)