Starting phenix.real_space_refine on Mon May 19 19:34:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lod_0936/05_2025/6lod_0936.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lod_0936/05_2025/6lod_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6lod_0936/05_2025/6lod_0936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lod_0936/05_2025/6lod_0936.map" model { file = "/net/cci-nas-00/data/ceres_data/6lod_0936/05_2025/6lod_0936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lod_0936/05_2025/6lod_0936.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.22, per 1000 atoms: 0.54 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: 5.57 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.88 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: 5.62 Time building geometry restraints manager: 5.86 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: 9767 17.48 - 34.96: 1120 34.96 - 52.45: 170 52.45 - 69.93: 40 69.93 - 87.41: 30 Dihedral angle restraints: 11127 sinusoidal: 4407 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 11124 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 45.290 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 15.534 87.409 6821 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.002 TRP C 186 HIS 0.007 0.002 HIS A 127 PHE 0.028 0.002 PHE C 266 TYR 0.026 0.002 TYR E 163 ARG 0.007 0.001 ARG B 990 Details of bonding type rmsd hydrogen bonds : bond 0.28938 ( 677) hydrogen bonds : angle 11.93103 ( 1926) metal coordination : bond 0.32330 ( 15) metal coordination : angle 17.45305 ( 45) covalent geometry : bond 0.02513 (19374) covalent geometry : angle 1.33417 (26522) Misc. bond : bond 0.13279 ( 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 : 1.980 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: 0.8377 (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: 0.8320 (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: 0.7889 (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: 0.3330 time to fit residues: 218.2615 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 : 1.892 ------------------------------------------------------------------------------- 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: chunk 193 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 179 optimal weight: 0.2980 chunk 69 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 GLN A 87 ASN A 190 ASN A 199 GLN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 373 GLN B 378 HIS ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 GLN B 975 GLN C 79 ASN C 141 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C 262 HIS C 387 ASN D 174 GLN D 192 ASN ** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.131095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.105929 restraints weight = 25138.208| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.39 r_work: 0.2954 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.650 19407 Z= 0.269 Angle : 1.354 78.786 26567 Z= 0.453 Chirality : 0.057 1.758 2856 Planarity : 0.007 0.078 3339 Dihedral : 9.313 87.944 2657 Min Nonbonded Distance : 1.427 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.13 % Allowed : 11.69 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.15), residues: 2317 helix: -2.96 (0.12), residues: 1095 sheet: -2.91 (0.38), residues: 153 loop : -2.24 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 186 HIS 0.004 0.001 HIS A 127 PHE 0.018 0.002 PHE F 136 TYR 0.020 0.002 TYR F 109 ARG 0.009 0.001 ARG F 140 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 677) hydrogen bonds : angle 6.07196 ( 1926) metal coordination : bond 0.02402 ( 15) metal coordination : angle 20.36439 ( 45) covalent geometry : bond 0.00596 (19374) covalent geometry : angle 1.06369 (26522) Misc. bond : bond 0.22112 ( 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 413 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 372 time to evaluate : 1.883 Fit side-chains REVERT: A 13 ARG cc_start: 0.7768 (tpt90) cc_final: 0.6937 (tpp80) REVERT: B 597 ASN cc_start: 0.9135 (t0) cc_final: 0.8714 (t0) REVERT: B 694 VAL cc_start: 0.8357 (m) cc_final: 0.7929 (t) REVERT: B 844 ASP cc_start: 0.8140 (m-30) cc_final: 0.7905 (m-30) REVERT: B 865 ASN cc_start: 0.8517 (t0) cc_final: 0.8189 (t0) REVERT: B 920 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8939 (m-10) REVERT: B 968 ARG cc_start: 0.7906 (mtp-110) cc_final: 0.7500 (ttt180) REVERT: C 26 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7421 (tp30) REVERT: C 38 THR cc_start: 0.7586 (t) cc_final: 0.6772 (p) REVERT: C 113 GLN cc_start: 0.8177 (mt0) cc_final: 0.7875 (mt0) REVERT: C 228 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7233 (pt0) REVERT: C 284 LEU cc_start: 0.8835 (tt) cc_final: 0.8598 (tt) REVERT: C 311 MET cc_start: 0.8909 (ttp) cc_final: 0.8609 (ttp) REVERT: D 49 GLU cc_start: 0.8106 (mp0) cc_final: 0.7023 (mm-30) REVERT: D 61 GLU cc_start: 0.7015 (mp0) cc_final: 0.6792 (mp0) REVERT: E 146 MET cc_start: 0.8551 (ttm) cc_final: 0.8274 (ttm) REVERT: E 151 TYR cc_start: 0.8655 (m-80) cc_final: 0.8437 (m-80) REVERT: E 157 ASN cc_start: 0.8538 (m110) cc_final: 0.8176 (m-40) REVERT: E 167 TYR cc_start: 0.8819 (p90) cc_final: 0.7920 (p90) REVERT: F 209 MET cc_start: 0.8236 (tpp) cc_final: 0.7801 (ttt) outliers start: 41 outliers final: 27 residues processed: 401 average time/residue: 0.3286 time to fit residues: 198.5065 Evaluate side-chains 356 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 328 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER 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 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 71 VAL 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 263 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 361 VAL 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 119 VAL Chi-restraints excluded: chain F residue 21 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: chunk 155 optimal weight: 1.9990 chunk 220 optimal weight: 0.0070 chunk 157 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 224 optimal weight: 0.1980 chunk 116 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS ** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 GLN B 926 ASN B 936 ASN C 79 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS F 41 GLN F 44 HIS F 353 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109215 restraints weight = 24579.542| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.46 r_work: 0.3043 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.609 19407 Z= 0.162 Angle : 1.155 84.619 26567 Z= 0.382 Chirality : 0.052 1.464 2856 Planarity : 0.005 0.071 3339 Dihedral : 8.868 87.798 2657 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.39 % Allowed : 14.19 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.16), residues: 2317 helix: -2.04 (0.14), residues: 1091 sheet: -2.91 (0.39), residues: 145 loop : -1.97 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 186 HIS 0.005 0.001 HIS C 246 PHE 0.017 0.001 PHE C 279 TYR 0.029 0.002 TYR F 109 ARG 0.006 0.000 ARG C 222 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 677) hydrogen bonds : angle 5.43461 ( 1926) metal coordination : bond 0.01139 ( 15) metal coordination : angle 18.13729 ( 45) covalent geometry : bond 0.00372 (19374) covalent geometry : angle 0.88228 (26522) Misc. bond : bond 0.20316 ( 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 389 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 343 time to evaluate : 2.210 Fit side-chains REVERT: A 13 ARG cc_start: 0.7717 (tpt90) cc_final: 0.6854 (tpp80) REVERT: A 171 CYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8076 (p) REVERT: B 158 ASP cc_start: 0.8978 (t0) cc_final: 0.8029 (t0) REVERT: B 192 GLN cc_start: 0.7172 (mp10) cc_final: 0.6939 (mp10) REVERT: B 313 ARG cc_start: 0.8639 (ptm-80) cc_final: 0.8172 (ptm-80) REVERT: B 418 GLU cc_start: 0.7539 (tp30) cc_final: 0.7275 (tp30) REVERT: B 597 ASN cc_start: 0.9187 (t0) cc_final: 0.8297 (t0) REVERT: B 694 VAL cc_start: 0.8376 (m) cc_final: 0.7922 (t) REVERT: B 833 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8441 (mt-10) REVERT: B 843 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8449 (m90) REVERT: B 844 ASP cc_start: 0.8060 (m-30) cc_final: 0.7773 (m-30) REVERT: B 920 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8904 (m-10) REVERT: B 968 ARG cc_start: 0.7905 (mtp-110) cc_final: 0.7486 (ttt180) REVERT: C 14 MET cc_start: 0.7620 (ttt) cc_final: 0.7176 (tpt) REVERT: C 113 GLN cc_start: 0.7996 (mt0) cc_final: 0.7738 (mt0) REVERT: C 311 MET cc_start: 0.8904 (ttp) cc_final: 0.8644 (ttp) REVERT: D 34 LEU cc_start: 0.7952 (pp) cc_final: 0.7124 (tt) REVERT: D 49 GLU cc_start: 0.8052 (mp0) cc_final: 0.7104 (mm-30) REVERT: D 142 TYR cc_start: 0.7220 (t80) cc_final: 0.7002 (t80) REVERT: E 151 TYR cc_start: 0.8608 (m-80) cc_final: 0.8400 (m-80) REVERT: E 157 ASN cc_start: 0.8543 (m110) cc_final: 0.8121 (m-40) REVERT: E 167 TYR cc_start: 0.8723 (p90) cc_final: 0.7912 (p90) REVERT: F 28 MET cc_start: 0.6707 (tpt) cc_final: 0.6429 (tpt) REVERT: F 179 SER cc_start: 0.8794 (p) cc_final: 0.8512 (t) REVERT: F 209 MET cc_start: 0.8150 (tpp) cc_final: 0.7766 (ttt) outliers start: 46 outliers final: 29 residues processed: 374 average time/residue: 0.3129 time to fit residues: 177.8596 Evaluate side-chains 348 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 316 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain B residue 82 LEU 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 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 843 HIS 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 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 243 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 214 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN B 437 ASN B 651 GLN B 800 HIS ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 ASN C 79 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.131331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.106871 restraints weight = 24806.969| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.43 r_work: 0.3010 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.596 19407 Z= 0.201 Angle : 1.139 84.446 26567 Z= 0.387 Chirality : 0.053 1.443 2856 Planarity : 0.005 0.071 3339 Dihedral : 8.640 87.187 2657 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.43 % Allowed : 15.02 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.17), residues: 2317 helix: -1.56 (0.14), residues: 1091 sheet: -2.85 (0.40), residues: 145 loop : -1.83 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 186 HIS 0.004 0.001 HIS A 66 PHE 0.017 0.001 PHE C 279 TYR 0.018 0.002 TYR C 269 ARG 0.005 0.001 ARG B 871 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 677) hydrogen bonds : angle 5.15840 ( 1926) metal coordination : bond 0.01363 ( 15) metal coordination : angle 17.16212 ( 45) covalent geometry : bond 0.00479 (19374) covalent geometry : angle 0.89430 (26522) Misc. bond : bond 0.20407 ( 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 394 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 328 time to evaluate : 1.875 Fit side-chains REVERT: A 13 ARG cc_start: 0.7729 (tpt90) cc_final: 0.6845 (tpp80) REVERT: A 171 CYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8208 (p) REVERT: B 87 GLU cc_start: 0.7702 (mt-10) cc_final: 0.6112 (mt-10) REVERT: B 158 ASP cc_start: 0.8843 (t0) cc_final: 0.8324 (t0) REVERT: B 185 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7211 (mmm) REVERT: B 192 GLN cc_start: 0.7204 (mp10) cc_final: 0.6982 (mp10) REVERT: B 252 ARG cc_start: 0.7547 (ttm170) cc_final: 0.7303 (ttm170) REVERT: B 276 MET cc_start: 0.9277 (mmm) cc_final: 0.8983 (mtp) REVERT: B 313 ARG cc_start: 0.8673 (ptm-80) cc_final: 0.8131 (ptm-80) REVERT: B 418 GLU cc_start: 0.7600 (tp30) cc_final: 0.7311 (tp30) REVERT: B 597 ASN cc_start: 0.9162 (t0) cc_final: 0.8814 (t0) REVERT: B 694 VAL cc_start: 0.8448 (m) cc_final: 0.7983 (t) REVERT: B 820 MET cc_start: 0.8609 (ttt) cc_final: 0.8170 (ttp) REVERT: B 843 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.8414 (m90) REVERT: B 865 ASN cc_start: 0.8583 (t0) cc_final: 0.8265 (t0) REVERT: B 918 CYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8394 (t) REVERT: B 920 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.8926 (m-10) REVERT: B 968 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7514 (ttt180) REVERT: C 14 MET cc_start: 0.7645 (ttt) cc_final: 0.7212 (tpt) REVERT: C 113 GLN cc_start: 0.8057 (mt0) cc_final: 0.7796 (mt0) REVERT: C 207 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7146 (ttmm) REVERT: C 239 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8462 (m) REVERT: C 311 MET cc_start: 0.8915 (ttp) cc_final: 0.8589 (ttp) REVERT: D 34 LEU cc_start: 0.7941 (pp) cc_final: 0.7156 (tt) REVERT: D 41 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7564 (ttp80) REVERT: E 117 HIS cc_start: 0.9099 (OUTLIER) cc_final: 0.8090 (m90) REVERT: E 146 MET cc_start: 0.8505 (ttm) cc_final: 0.8116 (ttm) REVERT: E 151 TYR cc_start: 0.8684 (m-80) cc_final: 0.8439 (m-80) REVERT: E 167 TYR cc_start: 0.8848 (p90) cc_final: 0.8003 (p90) REVERT: F 28 MET cc_start: 0.6686 (tpt) cc_final: 0.6445 (tpt) REVERT: F 179 SER cc_start: 0.8848 (p) cc_final: 0.8562 (t) outliers start: 66 outliers final: 39 residues processed: 372 average time/residue: 0.3074 time to fit residues: 175.4565 Evaluate side-chains 359 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 208 LEU 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 697 GLU Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 843 HIS 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 B residue 920 PHE Chi-restraints excluded: chain B residue 951 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 119 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 243 LEU 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 E residue 61 LEU 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 E residue 117 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 Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 353 HIS Chi-restraints excluded: chain F residue 370 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: chunk 142 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 800 HIS B 936 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.106312 restraints weight = 24882.993| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.55 r_work: 0.2944 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.584 19407 Z= 0.192 Angle : 1.122 83.869 26567 Z= 0.380 Chirality : 0.053 1.470 2856 Planarity : 0.005 0.070 3339 Dihedral : 8.465 86.240 2657 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.12 % Allowed : 16.32 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.17), residues: 2317 helix: -1.22 (0.15), residues: 1090 sheet: -2.78 (0.41), residues: 145 loop : -1.74 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 53 HIS 0.004 0.001 HIS A 66 PHE 0.017 0.001 PHE C 279 TYR 0.034 0.002 TYR E 152 ARG 0.007 0.000 ARG B 636 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 677) hydrogen bonds : angle 5.00926 ( 1926) metal coordination : bond 0.01193 ( 15) metal coordination : angle 16.88185 ( 45) covalent geometry : bond 0.00457 (19374) covalent geometry : angle 0.88215 (26522) Misc. bond : bond 0.19182 ( 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 388 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 328 time to evaluate : 2.077 Fit side-chains REVERT: B 87 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6078 (mt-10) REVERT: B 158 ASP cc_start: 0.8817 (t0) cc_final: 0.8396 (t0) REVERT: B 192 GLN cc_start: 0.7226 (mp10) cc_final: 0.7003 (mp10) REVERT: B 276 MET cc_start: 0.9265 (mmm) cc_final: 0.8967 (mtp) REVERT: B 313 ARG cc_start: 0.8754 (ptm-80) cc_final: 0.8349 (ptm-80) REVERT: B 418 GLU cc_start: 0.7645 (tp30) cc_final: 0.7391 (tp30) REVERT: B 597 ASN cc_start: 0.9160 (t0) cc_final: 0.8825 (t0) REVERT: B 694 VAL cc_start: 0.8442 (m) cc_final: 0.7981 (t) REVERT: B 820 MET cc_start: 0.8785 (ttt) cc_final: 0.8403 (ttp) REVERT: B 822 MET cc_start: 0.8995 (tpp) cc_final: 0.8694 (tpt) REVERT: B 843 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8480 (m90) REVERT: B 865 ASN cc_start: 0.8576 (t0) cc_final: 0.8276 (t0) REVERT: B 918 CYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8385 (t) REVERT: B 920 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8922 (m-10) REVERT: B 968 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7549 (ttt180) REVERT: C 14 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7488 (tpt) REVERT: C 113 GLN cc_start: 0.8061 (mt0) cc_final: 0.7788 (mt0) REVERT: C 207 LYS cc_start: 0.7604 (ttmt) cc_final: 0.7153 (ttmm) REVERT: C 311 MET cc_start: 0.8955 (ttp) cc_final: 0.8651 (ttp) REVERT: D 34 LEU cc_start: 0.8009 (pp) cc_final: 0.7247 (tt) REVERT: D 49 GLU cc_start: 0.8322 (mp0) cc_final: 0.7186 (mm-30) REVERT: E 117 HIS cc_start: 0.9117 (OUTLIER) cc_final: 0.8169 (m90) REVERT: E 151 TYR cc_start: 0.8666 (m-80) cc_final: 0.8322 (m-80) REVERT: E 167 TYR cc_start: 0.8863 (p90) cc_final: 0.7977 (p90) REVERT: F 28 MET cc_start: 0.6714 (tpt) cc_final: 0.6495 (tpt) REVERT: F 179 SER cc_start: 0.8864 (p) cc_final: 0.8575 (t) REVERT: F 234 LYS cc_start: 0.8186 (ttmm) cc_final: 0.7517 (tmtt) outliers start: 60 outliers final: 43 residues processed: 370 average time/residue: 0.3045 time to fit residues: 172.5446 Evaluate side-chains 357 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 309 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 LEU 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 502 TYR 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 843 HIS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 LYS 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 920 PHE Chi-restraints excluded: chain B residue 931 GLN 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 119 ILE Chi-restraints excluded: chain C residue 243 LEU 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 E residue 61 LEU 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 E residue 117 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 Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 353 HIS 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: chunk 105 optimal weight: 1.9990 chunk 123 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 203 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN B 390 ASN B 437 ASN B 800 HIS B 936 ASN C 23 GLN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.132657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108969 restraints weight = 24826.243| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.37 r_work: 0.3110 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.551 19407 Z= 0.161 Angle : 1.092 83.761 26567 Z= 0.368 Chirality : 0.052 1.469 2856 Planarity : 0.005 0.068 3339 Dihedral : 8.252 86.388 2657 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.12 % Allowed : 17.20 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.17), residues: 2317 helix: -0.94 (0.15), residues: 1086 sheet: -2.74 (0.38), residues: 167 loop : -1.63 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 186 HIS 0.005 0.001 HIS C 246 PHE 0.015 0.001 PHE C 279 TYR 0.032 0.001 TYR E 152 ARG 0.007 0.000 ARG B 636 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 677) hydrogen bonds : angle 4.86848 ( 1926) metal coordination : bond 0.00861 ( 15) metal coordination : angle 16.43974 ( 45) covalent geometry : bond 0.00384 (19374) covalent geometry : angle 0.85811 (26522) Misc. bond : bond 0.17351 ( 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 408 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 348 time to evaluate : 1.910 Fit side-chains REVERT: A 186 GLU cc_start: 0.8811 (mp0) cc_final: 0.8600 (mp0) REVERT: A 217 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8315 (mt-10) REVERT: B 87 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6068 (mt-10) REVERT: B 158 ASP cc_start: 0.8767 (t0) cc_final: 0.8242 (t0) REVERT: B 172 THR cc_start: 0.8390 (t) cc_final: 0.8181 (p) REVERT: B 192 GLN cc_start: 0.7098 (mp10) cc_final: 0.6890 (mp10) REVERT: B 252 ARG cc_start: 0.7634 (ttm170) cc_final: 0.7415 (ttm170) REVERT: B 276 MET cc_start: 0.9225 (mmm) cc_final: 0.8888 (mtp) REVERT: B 313 ARG cc_start: 0.8665 (ptm-80) cc_final: 0.8155 (ptm-80) REVERT: B 418 GLU cc_start: 0.7414 (tp30) cc_final: 0.7178 (tp30) REVERT: B 580 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8673 (tp) REVERT: B 597 ASN cc_start: 0.9122 (t0) cc_final: 0.8766 (t0) REVERT: B 694 VAL cc_start: 0.8404 (m) cc_final: 0.7964 (t) REVERT: B 820 MET cc_start: 0.8533 (ttt) cc_final: 0.8118 (ttp) REVERT: B 843 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8577 (m90) REVERT: B 865 ASN cc_start: 0.8490 (t0) cc_final: 0.8228 (t0) REVERT: B 918 CYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8247 (t) REVERT: B 920 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8891 (m-10) REVERT: B 968 ARG cc_start: 0.7964 (mtp-110) cc_final: 0.7608 (ttt180) REVERT: C 186 TRP cc_start: 0.8391 (t60) cc_final: 0.8190 (t60) REVERT: C 207 LYS cc_start: 0.7838 (ttmt) cc_final: 0.7426 (ttmm) REVERT: C 311 MET cc_start: 0.8918 (ttp) cc_final: 0.8585 (ttp) REVERT: C 370 LYS cc_start: 0.8292 (tttp) cc_final: 0.7806 (mtmm) REVERT: D 34 LEU cc_start: 0.8014 (pp) cc_final: 0.7334 (tt) REVERT: D 160 PHE cc_start: 0.8103 (m-80) cc_final: 0.7850 (m-80) REVERT: E 117 HIS cc_start: 0.9000 (OUTLIER) cc_final: 0.8184 (m90) REVERT: E 151 TYR cc_start: 0.8562 (m-80) cc_final: 0.8299 (m-80) REVERT: E 152 TYR cc_start: 0.8686 (t80) cc_final: 0.8453 (t80) REVERT: E 167 TYR cc_start: 0.8938 (p90) cc_final: 0.8125 (p90) REVERT: F 9 LEU cc_start: 0.8549 (tp) cc_final: 0.8238 (tp) REVERT: F 234 LYS cc_start: 0.8081 (ttmm) cc_final: 0.7523 (tmtt) REVERT: F 282 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8789 (p) outliers start: 60 outliers final: 41 residues processed: 391 average time/residue: 0.3053 time to fit residues: 184.1880 Evaluate side-chains 373 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 326 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 LEU 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 502 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 580 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 843 HIS Chi-restraints excluded: chain B residue 859 THR 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 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 119 ILE Chi-restraints excluded: chain C residue 243 LEU 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 23 LEU Chi-restraints excluded: chain E residue 61 LEU 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 E residue 117 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 Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 353 HIS 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: chunk 87 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS B 437 ASN B 800 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.111538 restraints weight = 24251.907| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.29 r_work: 0.2998 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.556 19407 Z= 0.187 Angle : 1.102 83.756 26567 Z= 0.378 Chirality : 0.052 1.461 2856 Planarity : 0.005 0.069 3339 Dihedral : 8.254 87.144 2657 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.17 % Allowed : 17.88 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.17), residues: 2317 helix: -0.79 (0.15), residues: 1086 sheet: -2.71 (0.40), residues: 157 loop : -1.61 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 53 HIS 0.005 0.001 HIS C 246 PHE 0.021 0.001 PHE B 106 TYR 0.027 0.002 TYR E 152 ARG 0.007 0.000 ARG B 636 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 677) hydrogen bonds : angle 4.85205 ( 1926) metal coordination : bond 0.01132 ( 15) metal coordination : angle 16.26021 ( 45) covalent geometry : bond 0.00446 (19374) covalent geometry : angle 0.87610 (26522) Misc. bond : bond 0.17687 ( 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 389 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 328 time to evaluate : 1.984 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8759 (mp0) cc_final: 0.8529 (mp0) REVERT: B 87 GLU cc_start: 0.7560 (mt-10) cc_final: 0.5969 (mt-10) REVERT: B 158 ASP cc_start: 0.8772 (t0) cc_final: 0.8319 (t0) REVERT: B 172 THR cc_start: 0.8367 (t) cc_final: 0.8149 (p) REVERT: B 192 GLN cc_start: 0.7017 (mp10) cc_final: 0.6803 (mp10) REVERT: B 313 ARG cc_start: 0.8754 (ptm-80) cc_final: 0.8139 (ptm-80) REVERT: B 418 GLU cc_start: 0.7411 (tp30) cc_final: 0.7164 (tp30) REVERT: B 597 ASN cc_start: 0.9169 (t0) cc_final: 0.8895 (t0) REVERT: B 694 VAL cc_start: 0.8429 (m) cc_final: 0.7920 (t) REVERT: B 820 MET cc_start: 0.8668 (ttt) cc_final: 0.8289 (ttp) REVERT: B 843 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.8469 (m90) REVERT: B 865 ASN cc_start: 0.8557 (t0) cc_final: 0.8241 (t0) REVERT: B 918 CYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8358 (t) REVERT: B 920 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8897 (m-10) REVERT: B 968 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7512 (ttt180) REVERT: C 113 GLN cc_start: 0.8145 (mt0) cc_final: 0.7835 (mt0) REVERT: C 207 LYS cc_start: 0.7509 (ttmt) cc_final: 0.7049 (ttmm) REVERT: C 311 MET cc_start: 0.8935 (ttp) cc_final: 0.8651 (ttp) REVERT: C 370 LYS cc_start: 0.8289 (tttp) cc_final: 0.7695 (mttt) REVERT: D 34 LEU cc_start: 0.7924 (pp) cc_final: 0.7237 (tt) REVERT: D 41 ARG cc_start: 0.7994 (ttp-170) cc_final: 0.7628 (ttp-170) REVERT: D 49 GLU cc_start: 0.8264 (mp0) cc_final: 0.7029 (mm-30) REVERT: D 59 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7514 (tt) REVERT: E 117 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.8136 (m90) REVERT: E 151 TYR cc_start: 0.8560 (m-80) cc_final: 0.8241 (m-80) REVERT: E 167 TYR cc_start: 0.8904 (p90) cc_final: 0.8041 (p90) REVERT: F 9 LEU cc_start: 0.8533 (tp) cc_final: 0.8215 (tp) REVERT: F 234 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7465 (tmtt) REVERT: F 282 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8746 (p) outliers start: 61 outliers final: 46 residues processed: 368 average time/residue: 0.3058 time to fit residues: 172.2396 Evaluate side-chains 371 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 319 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 208 LEU 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 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 841 THR Chi-restraints excluded: chain B residue 843 HIS 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 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 119 ILE Chi-restraints excluded: chain C residue 243 LEU 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 D residue 23 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain E residue 61 LEU 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 E residue 117 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 Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 353 HIS Chi-restraints excluded: chain F residue 370 LEU 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: chunk 52 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 86 optimal weight: 0.0980 chunk 168 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN B 437 ASN B 800 HIS ** 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 = 0.3454 r_free = 0.3454 target = 0.135504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.112308 restraints weight = 24664.484| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.38 r_work: 0.3151 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.470 19407 Z= 0.142 Angle : 1.067 83.455 26567 Z= 0.363 Chirality : 0.051 1.481 2856 Planarity : 0.005 0.067 3339 Dihedral : 8.063 87.166 2657 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.70 % Allowed : 18.14 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.18), residues: 2317 helix: -0.53 (0.16), residues: 1085 sheet: -2.75 (0.38), residues: 171 loop : -1.51 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 53 HIS 0.006 0.001 HIS C 246 PHE 0.015 0.001 PHE C 173 TYR 0.034 0.001 TYR F 109 ARG 0.008 0.000 ARG B 636 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 677) hydrogen bonds : angle 4.74645 ( 1926) metal coordination : bond 0.00576 ( 15) metal coordination : angle 15.77423 ( 45) covalent geometry : bond 0.00334 (19374) covalent geometry : angle 0.84800 (26522) Misc. bond : bond 0.14145 ( 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 401 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 349 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7808 (tpt-90) cc_final: 0.7073 (tpp80) REVERT: B 87 GLU cc_start: 0.7473 (mt-10) cc_final: 0.5776 (mt-10) REVERT: B 93 VAL cc_start: 0.9016 (m) cc_final: 0.8802 (t) REVERT: B 158 ASP cc_start: 0.8699 (t0) cc_final: 0.8233 (t0) REVERT: B 276 MET cc_start: 0.9168 (mmm) cc_final: 0.8783 (mtp) REVERT: B 313 ARG cc_start: 0.8701 (ptm-80) cc_final: 0.8120 (ptm-80) REVERT: B 418 GLU cc_start: 0.7511 (tp30) cc_final: 0.7279 (tp30) REVERT: B 597 ASN cc_start: 0.9104 (t0) cc_final: 0.8815 (t0) REVERT: B 694 VAL cc_start: 0.8441 (m) cc_final: 0.7949 (t) REVERT: B 795 LEU cc_start: 0.8582 (mt) cc_final: 0.8332 (mt) REVERT: B 843 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8528 (m90) REVERT: B 918 CYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8239 (t) REVERT: B 920 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8801 (m-10) REVERT: B 968 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7591 (ttt180) REVERT: C 207 LYS cc_start: 0.7658 (ttmt) cc_final: 0.7221 (ttmm) REVERT: C 311 MET cc_start: 0.8974 (ttp) cc_final: 0.8566 (ttm) REVERT: C 370 LYS cc_start: 0.8404 (tttp) cc_final: 0.7794 (mttt) REVERT: D 34 LEU cc_start: 0.7842 (pp) cc_final: 0.7247 (tt) REVERT: D 41 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.7629 (ttp-170) REVERT: D 49 GLU cc_start: 0.8300 (mp0) cc_final: 0.7129 (mm-30) REVERT: D 59 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7727 (tt) REVERT: E 117 HIS cc_start: 0.8901 (OUTLIER) cc_final: 0.7932 (m90) REVERT: E 151 TYR cc_start: 0.8546 (m-80) cc_final: 0.8257 (m-80) REVERT: E 167 TYR cc_start: 0.8885 (p90) cc_final: 0.7984 (p90) REVERT: F 9 LEU cc_start: 0.8539 (tp) cc_final: 0.8220 (tp) REVERT: F 234 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7415 (tmtt) REVERT: F 343 ILE cc_start: 0.8865 (mm) cc_final: 0.8550 (mm) outliers start: 52 outliers final: 36 residues processed: 385 average time/residue: 0.2988 time to fit residues: 176.9791 Evaluate side-chains 368 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 327 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 208 LEU 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 502 TYR Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 843 HIS 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 14 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 243 LEU 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 D residue 23 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 117 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 Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 353 HIS Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 186 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 473 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.134055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.110466 restraints weight = 24681.020| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.34 r_work: 0.3061 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.495 19407 Z= 0.167 Angle : 1.074 83.450 26567 Z= 0.371 Chirality : 0.052 1.511 2856 Planarity : 0.005 0.068 3339 Dihedral : 8.042 88.267 2657 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.55 % Allowed : 18.40 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.18), residues: 2317 helix: -0.46 (0.16), residues: 1089 sheet: -2.60 (0.39), residues: 167 loop : -1.48 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 53 HIS 0.005 0.001 HIS C 246 PHE 0.019 0.001 PHE C 279 TYR 0.039 0.001 TYR F 109 ARG 0.007 0.000 ARG B 558 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 677) hydrogen bonds : angle 4.73024 ( 1926) metal coordination : bond 0.00945 ( 15) metal coordination : angle 15.53122 ( 45) covalent geometry : bond 0.00400 (19374) covalent geometry : angle 0.86436 (26522) Misc. bond : bond 0.15485 ( 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 379 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 330 time to evaluate : 1.849 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7778 (tpt-90) cc_final: 0.7032 (tpp80) REVERT: A 191 MET cc_start: 0.8915 (mmm) cc_final: 0.8500 (mmp) REVERT: B 87 GLU cc_start: 0.7483 (mt-10) cc_final: 0.5865 (mt-10) REVERT: B 93 VAL cc_start: 0.9031 (m) cc_final: 0.8793 (t) REVERT: B 158 ASP cc_start: 0.8760 (t0) cc_final: 0.8325 (t0) REVERT: B 276 MET cc_start: 0.9179 (mmm) cc_final: 0.8808 (mtp) REVERT: B 313 ARG cc_start: 0.8724 (ptm-80) cc_final: 0.8085 (ptm-80) REVERT: B 418 GLU cc_start: 0.7517 (tp30) cc_final: 0.7282 (tp30) REVERT: B 597 ASN cc_start: 0.9140 (t0) cc_final: 0.8896 (t0) REVERT: B 694 VAL cc_start: 0.8439 (m) cc_final: 0.7925 (t) REVERT: B 795 LEU cc_start: 0.8602 (mt) cc_final: 0.8333 (mt) REVERT: B 820 MET cc_start: 0.8645 (ttt) cc_final: 0.8383 (ttp) REVERT: B 822 MET cc_start: 0.8908 (tpp) cc_final: 0.8476 (mmm) REVERT: B 865 ASN cc_start: 0.8518 (t0) cc_final: 0.8231 (t0) REVERT: B 918 CYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8314 (t) REVERT: B 920 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8855 (m-10) REVERT: B 968 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7549 (ttt180) REVERT: C 207 LYS cc_start: 0.7551 (ttmt) cc_final: 0.7095 (ttmm) REVERT: C 311 MET cc_start: 0.8963 (ttp) cc_final: 0.8732 (ttp) REVERT: C 370 LYS cc_start: 0.8414 (tttp) cc_final: 0.7743 (mttt) REVERT: D 34 LEU cc_start: 0.7804 (pp) cc_final: 0.7236 (tt) REVERT: D 41 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7564 (ttp-170) REVERT: D 49 GLU cc_start: 0.8297 (mp0) cc_final: 0.7102 (mm-30) REVERT: D 59 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7671 (tt) REVERT: E 117 HIS cc_start: 0.8991 (OUTLIER) cc_final: 0.8031 (m90) REVERT: E 151 TYR cc_start: 0.8552 (m-80) cc_final: 0.8246 (m-80) REVERT: E 167 TYR cc_start: 0.8857 (p90) cc_final: 0.8006 (p90) REVERT: F 9 LEU cc_start: 0.8499 (tp) cc_final: 0.8180 (tp) REVERT: F 234 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7418 (tmtt) REVERT: F 343 ILE cc_start: 0.8870 (mm) cc_final: 0.8598 (mm) outliers start: 49 outliers final: 42 residues processed: 365 average time/residue: 0.2923 time to fit residues: 164.1202 Evaluate side-chains 372 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 326 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 208 LEU 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 502 TYR Chi-restraints excluded: chain B residue 563 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 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 49 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 264 THR 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 23 LEU 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 E residue 117 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 Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 353 HIS Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.9647 > 50: distance: 89 - 111: 8.243 distance: 93 - 116: 24.675 distance: 97 - 130: 28.768 distance: 102 - 111: 7.633 distance: 103 - 138: 18.049 distance: 111 - 112: 18.525 distance: 112 - 113: 12.243 distance: 112 - 115: 25.356 distance: 113 - 114: 14.607 distance: 113 - 116: 23.860 distance: 116 - 117: 10.194 distance: 117 - 118: 10.075 distance: 117 - 120: 37.332 distance: 118 - 119: 23.221 distance: 118 - 130: 29.965 distance: 120 - 121: 17.170 distance: 121 - 122: 23.240 distance: 121 - 123: 11.968 distance: 122 - 124: 18.345 distance: 123 - 125: 7.428 distance: 125 - 127: 5.823 distance: 126 - 128: 5.440 distance: 127 - 129: 4.985 distance: 128 - 129: 6.793 distance: 130 - 131: 10.651 distance: 131 - 132: 19.040 distance: 131 - 134: 30.970 distance: 132 - 133: 21.652 distance: 132 - 138: 13.186 distance: 134 - 135: 23.835 distance: 135 - 136: 29.177 distance: 135 - 137: 27.904 distance: 138 - 139: 25.819 distance: 139 - 140: 20.647 distance: 139 - 142: 31.667 distance: 140 - 141: 23.752 distance: 140 - 146: 13.493 distance: 142 - 143: 27.781 distance: 143 - 144: 32.762 distance: 143 - 145: 35.554 distance: 146 - 147: 17.291 distance: 147 - 148: 8.302 distance: 147 - 150: 34.831 distance: 148 - 149: 24.774 distance: 148 - 155: 28.264 distance: 150 - 151: 38.572 distance: 151 - 152: 26.398 distance: 152 - 153: 16.999 distance: 152 - 154: 13.522 distance: 155 - 156: 12.722 distance: 156 - 157: 45.461 distance: 156 - 159: 16.295 distance: 157 - 158: 56.307 distance: 157 - 166: 20.284 distance: 159 - 160: 9.628 distance: 160 - 161: 19.280 distance: 161 - 162: 9.134 distance: 162 - 163: 23.686 distance: 163 - 164: 15.640 distance: 163 - 165: 14.457 distance: 166 - 167: 38.754 distance: 167 - 168: 22.371 distance: 167 - 170: 55.197 distance: 168 - 169: 35.987 distance: 168 - 171: 27.523 distance: 171 - 172: 9.132 distance: 171 - 177: 30.511 distance: 172 - 173: 21.851 distance: 172 - 175: 39.123 distance: 173 - 174: 52.075 distance: 173 - 178: 18.492 distance: 175 - 176: 16.781 distance: 176 - 177: 50.357 distance: 178 - 179: 31.442 distance: 179 - 180: 51.841 distance: 179 - 182: 52.378 distance: 180 - 181: 24.434 distance: 180 - 186: 15.202 distance: 182 - 183: 59.205 distance: 183 - 184: 42.456 distance: 183 - 185: 44.349 distance: 186 - 187: 33.702 distance: 187 - 188: 23.646 distance: 187 - 190: 31.801 distance: 188 - 189: 26.357 distance: 188 - 194: 33.222 distance: 190 - 191: 20.750 distance: 191 - 192: 20.974 distance: 191 - 193: 18.489