Starting phenix.real_space_refine on Sat Aug 23 15:55:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5t_35993/08_2025/8j5t_35993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5t_35993/08_2025/8j5t_35993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j5t_35993/08_2025/8j5t_35993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5t_35993/08_2025/8j5t_35993.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5t_35993/08_2025/8j5t_35993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5t_35993/08_2025/8j5t_35993.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.080 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 6 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 8378 2.51 5 N 2359 2.21 5 O 2443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13234 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3947 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 28, 'TRANS': 490} Chain: "B" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2475 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain: "C" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2185 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain: "D" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4555 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 35, 'TRANS': 572} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {' MG': 2, 'ATP': 2, 'SF4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10760 SG CYS D 292 57.075 44.527 16.961 1.00 73.85 S ATOM 10813 SG CYS D 299 62.442 47.997 16.652 1.00 84.80 S ATOM 10713 SG CYS D 286 58.566 48.547 21.699 1.00 77.21 S ATOM 10946 SG CYS D 317 56.814 50.799 15.887 1.00 80.19 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER A 195 " occ=0.47 ... (4 atoms not shown) pdb=" OG SER A 195 " occ=0.47 residue: pdb=" N GLY A 509 " occ=0.48 ... (2 atoms not shown) pdb=" O GLY A 509 " occ=0.48 residue: pdb=" N GLU A 510 " occ=0.48 ... (7 atoms not shown) pdb=" OE2 GLU A 510 " occ=0.48 residue: pdb=" N SER A 511 " occ=0.48 ... (4 atoms not shown) pdb=" OG SER A 511 " occ=0.48 Time building chain proxies: 3.28, per 1000 atoms: 0.25 Number of scatterers: 13234 At special positions: 0 Unit cell: (85.696, 89.856, 163.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 42 16.00 P 6 15.00 Mg 2 11.99 O 2443 8.00 N 2359 7.00 C 8378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 769.8 milliseconds Enol-peptide restraints added in 1.7 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 705 " pdb="FE2 SF4 D 705 " - pdb=" SG CYS D 299 " pdb="FE1 SF4 D 705 " - pdb=" SG CYS D 292 " pdb="FE4 SF4 D 705 " - pdb=" SG CYS D 317 " pdb="FE3 SF4 D 705 " - pdb=" SG CYS D 286 " Number of angles added : 12 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 12 sheets defined 49.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 171 through 182 removed outlier: 4.121A pdb=" N ILE A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 223 through 227 removed outlier: 4.204A pdb=" N PHE A 227 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 296 through 306 removed outlier: 4.680A pdb=" N LEU A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix removed outlier: 3.663A pdb=" N ASN A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 375 Processing helix chain 'A' and resid 407 through 417 removed outlier: 3.986A pdb=" N ALA A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 459 removed outlier: 3.812A pdb=" N THR A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 459 " --> pdb=" O HIS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 removed outlier: 4.060A pdb=" N LEU A 501 " --> pdb=" O PRO A 497 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.805A pdb=" N ARG A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 550 Processing helix chain 'B' and resid 2 through 31 removed outlier: 4.191A pdb=" N LEU B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TYR B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.633A pdb=" N MET B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.665A pdb=" N LYS B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 74 removed outlier: 3.706A pdb=" N HIS B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 123 removed outlier: 5.274A pdb=" N VAL B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 141 Processing helix chain 'B' and resid 143 through 163 Processing helix chain 'B' and resid 182 through 192 Processing helix chain 'B' and resid 192 through 219 removed outlier: 3.899A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.708A pdb=" N GLY B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 4.275A pdb=" N ARG B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 4.127A pdb=" N LEU B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 removed outlier: 3.582A pdb=" N ILE B 271 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 288 removed outlier: 3.518A pdb=" N VAL B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 305 removed outlier: 3.702A pdb=" N VAL B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 319 Processing helix chain 'C' and resid 6 through 16 removed outlier: 3.563A pdb=" N LEU C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 38 removed outlier: 4.937A pdb=" N LEU C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 110 removed outlier: 3.620A pdb=" N LYS C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 127 Processing helix chain 'C' and resid 128 through 137 removed outlier: 3.946A pdb=" N LEU C 132 " --> pdb=" O PRO C 128 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 137 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 156 removed outlier: 3.819A pdb=" N ILE C 146 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 173 removed outlier: 3.712A pdb=" N SER C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.964A pdb=" N ARG C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 225 removed outlier: 3.553A pdb=" N ILE C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Proline residue: C 198 - end of helix removed outlier: 4.867A pdb=" N SER C 202 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 204 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 245 through 248 removed outlier: 4.573A pdb=" N THR C 248 " --> pdb=" O ALA C 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 245 through 248' Processing helix chain 'C' and resid 250 through 280 removed outlier: 4.159A pdb=" N PHE C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) Proline residue: C 257 - end of helix removed outlier: 3.548A pdb=" N GLY C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.784A pdb=" N MET D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 107 through 119 removed outlier: 4.452A pdb=" N HIS D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 149 through 150 No H-bonds generated for 'chain 'D' and resid 149 through 150' Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.794A pdb=" N VAL D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 203 removed outlier: 4.330A pdb=" N GLN D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 removed outlier: 3.542A pdb=" N GLU D 220 " --> pdb=" O GLY D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 removed outlier: 3.574A pdb=" N TYR D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.518A pdb=" N GLY D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 399 through 409 removed outlier: 3.571A pdb=" N LEU D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU D 409 " --> pdb=" O HIS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 437 Processing helix chain 'D' and resid 456 through 463 Processing helix chain 'D' and resid 464 through 467 Processing helix chain 'D' and resid 473 through 486 removed outlier: 3.884A pdb=" N ASP D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.609A pdb=" N PHE D 500 " --> pdb=" O PRO D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 531 through 548 removed outlier: 3.627A pdb=" N GLY D 537 " --> pdb=" O SER D 533 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN D 548 " --> pdb=" O ASP D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 595 through 601 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 95 removed outlier: 6.300A pdb=" N THR A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL A 262 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 146 removed outlier: 4.044A pdb=" N SER A 143 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLN A 211 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG A 205 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 213 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 203 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR A 215 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 468 removed outlier: 6.080A pdb=" N ASP A 438 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 465 through 468 removed outlier: 6.080A pdb=" N ASP A 438 " --> pdb=" O GLN A 467 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER A 338 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN A 559 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR A 340 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 421 through 423 removed outlier: 3.659A pdb=" N SER A 423 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A 426 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA9, first strand: chain 'D' and resid 21 through 31 removed outlier: 6.566A pdb=" N ALA D 23 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR D 13 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG D 25 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA D 11 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE D 27 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 92 through 94 removed outlier: 6.479A pdb=" N GLY D 92 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP D 179 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL D 94 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU D 176 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE D 211 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N CYS D 178 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL D 36 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU D 226 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA D 38 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET D 228 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL D 40 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA D 225 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER D 236 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 227 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 369 through 384 removed outlier: 6.649A pdb=" N LEU D 361 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU D 373 " --> pdb=" O TYR D 359 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR D 359 " --> pdb=" O GLU D 373 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ARG D 375 " --> pdb=" O LYS D 357 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS D 357 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL D 377 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU D 355 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY D 379 " --> pdb=" O ARG D 353 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ARG D 353 " --> pdb=" O GLY D 379 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N SER D 381 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ARG D 351 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 441 through 443 removed outlier: 6.453A pdb=" N LEU D 574 " --> pdb=" O VAL D 578 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1707 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: 2.51 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 5287 1.39 - 1.61: 8120 1.61 - 1.84: 68 1.84 - 2.06: 0 2.06 - 2.29: 12 Bond restraints: 13487 Sorted by residual: bond pdb=" C4 ATP D 703 " pdb=" C5 ATP D 703 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.57e+01 bond pdb=" C4 ATP D 701 " pdb=" C5 ATP D 701 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.36e+01 bond pdb=" C5 ATP D 701 " pdb=" C6 ATP D 701 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.30e+01 bond pdb=" C5 ATP D 703 " pdb=" C6 ATP D 703 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.99e+01 bond pdb=" C ALA A 450 " pdb=" O ALA A 450 " ideal model delta sigma weight residual 1.237 1.167 0.069 1.17e-02 7.31e+03 3.51e+01 ... (remaining 13482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 18161 3.50 - 7.01: 195 7.01 - 10.51: 22 10.51 - 14.02: 4 14.02 - 17.52: 2 Bond angle restraints: 18384 Sorted by residual: angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 122.35 17.52 1.00e+00 1.00e+00 3.07e+02 angle pdb=" PB ATP D 703 " pdb=" O3B ATP D 703 " pdb=" PG ATP D 703 " ideal model delta sigma weight residual 139.87 122.89 16.98 1.00e+00 1.00e+00 2.88e+02 angle pdb=" N VAL B 181 " pdb=" CA VAL B 181 " pdb=" C VAL B 181 " ideal model delta sigma weight residual 113.71 102.08 11.63 9.50e-01 1.11e+00 1.50e+02 angle pdb=" PA ATP D 703 " pdb=" O3A ATP D 703 " pdb=" PB ATP D 703 " ideal model delta sigma weight residual 136.83 125.12 11.71 1.00e+00 1.00e+00 1.37e+02 angle pdb=" PA ATP D 701 " pdb=" O3A ATP D 701 " pdb=" PB ATP D 701 " ideal model delta sigma weight residual 136.83 127.87 8.96 1.00e+00 1.00e+00 8.03e+01 ... (remaining 18379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7042 17.98 - 35.95: 839 35.95 - 53.93: 174 53.93 - 71.90: 31 71.90 - 89.87: 12 Dihedral angle restraints: 8098 sinusoidal: 3152 harmonic: 4946 Sorted by residual: dihedral pdb=" CA TYR A 406 " pdb=" C TYR A 406 " pdb=" N ASN A 407 " pdb=" CA ASN A 407 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLU D 594 " pdb=" C GLU D 594 " pdb=" N TYR D 595 " pdb=" CA TYR D 595 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C ARG A 447 " pdb=" N ARG A 447 " pdb=" CA ARG A 447 " pdb=" CB ARG A 447 " ideal model delta harmonic sigma weight residual -122.60 -110.95 -11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 8095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1826 0.071 - 0.141: 307 0.141 - 0.212: 25 0.212 - 0.283: 5 0.283 - 0.353: 3 Chirality restraints: 2166 Sorted by residual: chirality pdb=" CA ARG A 447 " pdb=" N ARG A 447 " pdb=" C ARG A 447 " pdb=" CB ARG A 447 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA TRP B 182 " pdb=" N TRP B 182 " pdb=" C TRP B 182 " pdb=" CB TRP B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ALA A 443 " pdb=" N ALA A 443 " pdb=" C ALA A 443 " pdb=" CB ALA A 443 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 2163 not shown) Planarity restraints: 2370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 123 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ARG B 123 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG B 123 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN B 124 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 38 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C MET B 38 " 0.055 2.00e-02 2.50e+03 pdb=" O MET B 38 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN B 39 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 151 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C LEU C 151 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU C 151 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 152 " 0.017 2.00e-02 2.50e+03 ... (remaining 2367 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 123 2.58 - 3.16: 11371 3.16 - 3.74: 19833 3.74 - 4.32: 29245 4.32 - 4.90: 48819 Nonbonded interactions: 109391 Sorted by model distance: nonbonded pdb=" OE1 GLN D 96 " pdb="MG MG D 704 " model vdw 2.004 2.170 nonbonded pdb=" O3G ATP D 701 " pdb="MG MG D 702 " model vdw 2.061 2.170 nonbonded pdb=" OG SER D 48 " pdb="MG MG D 704 " model vdw 2.066 2.170 nonbonded pdb=" O1G ATP D 703 " pdb="MG MG D 704 " model vdw 2.124 2.170 nonbonded pdb=" O PHE B 254 " pdb=" N GLY B 257 " model vdw 2.208 3.120 ... (remaining 109386 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=0.47 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: 2.690 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.000 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 13491 Z= 0.412 Angle : 0.961 17.519 18396 Z= 0.617 Chirality : 0.054 0.353 2166 Planarity : 0.007 0.106 2370 Dihedral : 16.081 89.875 4926 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.65 % Allowed : 1.38 % Favored : 97.96 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.19), residues: 1732 helix: -1.22 (0.17), residues: 807 sheet: -1.53 (0.41), residues: 165 loop : -1.93 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 421 TYR 0.017 0.002 TYR A 441 PHE 0.018 0.002 PHE A 440 TRP 0.013 0.002 TRP A 339 HIS 0.013 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00730 (13487) covalent geometry : angle 0.96159 (18384) hydrogen bonds : bond 0.18089 ( 593) hydrogen bonds : angle 7.39174 ( 1707) metal coordination : bond 0.03084 ( 4) metal coordination : angle 0.02458 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.572 Fit side-chains REVERT: A 442 ASP cc_start: 0.7813 (t0) cc_final: 0.7335 (t70) REVERT: B 7 ARG cc_start: 0.7583 (ttt180) cc_final: 0.7353 (ttm170) REVERT: D 63 GLN cc_start: 0.8003 (tt0) cc_final: 0.7523 (tm-30) REVERT: D 65 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7545 (ttp80) REVERT: D 360 ARG cc_start: 0.7514 (ttp80) cc_final: 0.6983 (ptp-110) REVERT: D 409 GLU cc_start: 0.7723 (pp20) cc_final: 0.7412 (pp20) outliers start: 9 outliers final: 5 residues processed: 165 average time/residue: 0.6341 time to fit residues: 114.5850 Evaluate side-chains 127 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 39 GLN B 190 GLN ** D 506 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 = 0.3342 r_free = 0.3342 target = 0.107060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.090589 restraints weight = 20402.939| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.05 r_work: 0.2971 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13491 Z= 0.140 Angle : 0.644 10.744 18396 Z= 0.328 Chirality : 0.043 0.158 2166 Planarity : 0.005 0.058 2370 Dihedral : 8.505 107.313 1985 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.82 % Allowed : 10.33 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.19), residues: 1732 helix: -0.39 (0.18), residues: 810 sheet: -1.62 (0.40), residues: 170 loop : -1.63 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 69 TYR 0.014 0.001 TYR A 156 PHE 0.010 0.001 PHE D 151 TRP 0.010 0.001 TRP C 119 HIS 0.008 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00317 (13487) covalent geometry : angle 0.63678 (18384) hydrogen bonds : bond 0.04786 ( 593) hydrogen bonds : angle 5.22266 ( 1707) metal coordination : bond 0.00919 ( 4) metal coordination : angle 3.85546 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.533 Fit side-chains REVERT: A 442 ASP cc_start: 0.8036 (t0) cc_final: 0.7448 (t70) REVERT: B 95 ILE cc_start: 0.8597 (pt) cc_final: 0.8388 (mt) REVERT: C 47 ASP cc_start: 0.8485 (p0) cc_final: 0.8170 (p0) REVERT: D 63 GLN cc_start: 0.8367 (tt0) cc_final: 0.7748 (tm-30) REVERT: D 65 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8098 (ttp80) REVERT: D 248 MET cc_start: 0.7625 (tpt) cc_final: 0.6586 (tpt) REVERT: D 269 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8279 (pp) REVERT: D 360 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7525 (ptt180) REVERT: D 409 GLU cc_start: 0.8349 (pp20) cc_final: 0.7924 (pp20) REVERT: D 423 THR cc_start: 0.8715 (p) cc_final: 0.8465 (t) REVERT: D 592 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8459 (mmpt) outliers start: 25 outliers final: 7 residues processed: 160 average time/residue: 0.5212 time to fit residues: 92.1684 Evaluate side-chains 133 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 583 ASP Chi-restraints excluded: chain D residue 592 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 38 optimal weight: 5.9990 chunk 140 optimal weight: 0.0870 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN B 39 GLN B 191 HIS B 211 GLN C 211 ASN D 441 GLN D 476 HIS ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.092513 restraints weight = 20539.146| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.11 r_work: 0.2983 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13491 Z= 0.118 Angle : 0.589 9.769 18396 Z= 0.297 Chirality : 0.042 0.145 2166 Planarity : 0.004 0.055 2370 Dihedral : 7.791 80.163 1980 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.25 % Allowed : 13.75 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.20), residues: 1732 helix: 0.09 (0.18), residues: 808 sheet: -1.42 (0.41), residues: 170 loop : -1.55 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 8 TYR 0.013 0.001 TYR A 156 PHE 0.011 0.001 PHE B 272 TRP 0.009 0.001 TRP C 119 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00268 (13487) covalent geometry : angle 0.57836 (18384) hydrogen bonds : bond 0.04108 ( 593) hydrogen bonds : angle 4.80730 ( 1707) metal coordination : bond 0.00878 ( 4) metal coordination : angle 4.32319 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.552 Fit side-chains REVERT: C 16 LEU cc_start: 0.8518 (pp) cc_final: 0.8241 (mt) REVERT: C 47 ASP cc_start: 0.8526 (p0) cc_final: 0.8258 (p0) REVERT: C 147 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6564 (mmp) REVERT: D 63 GLN cc_start: 0.8362 (tt0) cc_final: 0.7700 (tm-30) REVERT: D 99 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7554 (tmt) REVERT: D 248 MET cc_start: 0.7738 (tpt) cc_final: 0.6532 (tpt) REVERT: D 260 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7610 (ttm110) REVERT: D 360 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7522 (ptt180) REVERT: D 409 GLU cc_start: 0.8338 (pp20) cc_final: 0.7868 (pp20) REVERT: D 423 THR cc_start: 0.8544 (p) cc_final: 0.8295 (t) REVERT: D 446 ASP cc_start: 0.8055 (t70) cc_final: 0.7827 (p0) REVERT: D 452 ASP cc_start: 0.8385 (p0) cc_final: 0.8072 (p0) REVERT: D 592 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8372 (mmmt) outliers start: 31 outliers final: 12 residues processed: 160 average time/residue: 0.5267 time to fit residues: 93.4019 Evaluate side-chains 145 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 592 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 89 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.088911 restraints weight = 20523.837| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.07 r_work: 0.2939 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13491 Z= 0.177 Angle : 0.620 9.809 18396 Z= 0.312 Chirality : 0.044 0.154 2166 Planarity : 0.005 0.055 2370 Dihedral : 7.552 88.183 1980 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.98 % Allowed : 15.35 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.20), residues: 1732 helix: 0.21 (0.18), residues: 808 sheet: -1.26 (0.41), residues: 173 loop : -1.61 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 8 TYR 0.014 0.001 TYR A 156 PHE 0.013 0.001 PHE B 272 TRP 0.011 0.001 TRP A 339 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00424 (13487) covalent geometry : angle 0.60964 (18384) hydrogen bonds : bond 0.04398 ( 593) hydrogen bonds : angle 4.74138 ( 1707) metal coordination : bond 0.01043 ( 4) metal coordination : angle 4.50899 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.567 Fit side-chains REVERT: C 16 LEU cc_start: 0.8522 (pp) cc_final: 0.8281 (mt) REVERT: D 63 GLN cc_start: 0.8348 (tt0) cc_final: 0.7737 (tm-30) REVERT: D 65 ARG cc_start: 0.8489 (ttp80) cc_final: 0.7975 (ttp80) REVERT: D 248 MET cc_start: 0.7828 (tpt) cc_final: 0.6558 (tpt) REVERT: D 269 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8236 (pp) REVERT: D 360 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7587 (ptt180) REVERT: D 409 GLU cc_start: 0.8352 (pp20) cc_final: 0.7937 (pp20) REVERT: D 415 SER cc_start: 0.8765 (t) cc_final: 0.8505 (t) REVERT: D 423 THR cc_start: 0.8555 (p) cc_final: 0.8317 (t) outliers start: 41 outliers final: 20 residues processed: 163 average time/residue: 0.5618 time to fit residues: 101.2087 Evaluate side-chains 148 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 583 ASP Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 592 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 76 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 152 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.2244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 68 ASN C 211 ASN ** D 506 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 = 0.3334 r_free = 0.3334 target = 0.106489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.089834 restraints weight = 20556.641| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.07 r_work: 0.2957 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13491 Z= 0.140 Angle : 0.594 9.410 18396 Z= 0.295 Chirality : 0.042 0.147 2166 Planarity : 0.004 0.055 2370 Dihedral : 7.241 72.842 1980 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.76 % Allowed : 16.95 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.20), residues: 1732 helix: 0.33 (0.19), residues: 810 sheet: -1.16 (0.40), residues: 187 loop : -1.49 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 8 TYR 0.013 0.001 TYR A 156 PHE 0.011 0.001 PHE B 223 TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00329 (13487) covalent geometry : angle 0.58232 (18384) hydrogen bonds : bond 0.04016 ( 593) hydrogen bonds : angle 4.62117 ( 1707) metal coordination : bond 0.00873 ( 4) metal coordination : angle 4.54360 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.545 Fit side-chains REVERT: A 331 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8951 (mt) REVERT: C 47 ASP cc_start: 0.8498 (p0) cc_final: 0.8270 (p0) REVERT: D 63 GLN cc_start: 0.8355 (tt0) cc_final: 0.7724 (tm-30) REVERT: D 65 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7934 (ttp80) REVERT: D 248 MET cc_start: 0.7822 (tpt) cc_final: 0.6527 (tpt) REVERT: D 269 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8247 (pp) REVERT: D 360 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7560 (ptt180) REVERT: D 409 GLU cc_start: 0.8335 (pp20) cc_final: 0.7940 (pp20) REVERT: D 415 SER cc_start: 0.8755 (t) cc_final: 0.8492 (t) REVERT: D 423 THR cc_start: 0.8532 (p) cc_final: 0.8311 (t) REVERT: D 545 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8749 (tt) outliers start: 38 outliers final: 19 residues processed: 159 average time/residue: 0.5614 time to fit residues: 99.3242 Evaluate side-chains 147 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 583 ASP Chi-restraints excluded: chain D residue 592 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 145 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 68 ASN C 211 ASN ** D 506 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 = 0.3332 r_free = 0.3332 target = 0.106353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.089687 restraints weight = 20533.262| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.07 r_work: 0.2955 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13491 Z= 0.145 Angle : 0.592 9.462 18396 Z= 0.295 Chirality : 0.042 0.146 2166 Planarity : 0.004 0.055 2370 Dihedral : 7.120 68.480 1980 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.13 % Allowed : 17.53 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.20), residues: 1732 helix: 0.39 (0.19), residues: 811 sheet: -1.19 (0.39), residues: 193 loop : -1.47 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 8 TYR 0.013 0.001 TYR A 156 PHE 0.011 0.001 PHE B 223 TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00345 (13487) covalent geometry : angle 0.58122 (18384) hydrogen bonds : bond 0.03938 ( 593) hydrogen bonds : angle 4.56715 ( 1707) metal coordination : bond 0.00845 ( 4) metal coordination : angle 4.53725 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.518 Fit side-chains REVERT: A 300 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8190 (mtp85) REVERT: C 1 MET cc_start: 0.7233 (tpt) cc_final: 0.6972 (tmm) REVERT: C 47 ASP cc_start: 0.8510 (p0) cc_final: 0.8290 (p0) REVERT: D 63 GLN cc_start: 0.8339 (tt0) cc_final: 0.7702 (tm-30) REVERT: D 65 ARG cc_start: 0.8393 (ttp80) cc_final: 0.7882 (ttp80) REVERT: D 99 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7676 (tmt) REVERT: D 235 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: D 248 MET cc_start: 0.7853 (tpt) cc_final: 0.6549 (tpt) REVERT: D 269 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8279 (pp) REVERT: D 360 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7560 (ptt180) REVERT: D 409 GLU cc_start: 0.8328 (pp20) cc_final: 0.7927 (pp20) REVERT: D 415 SER cc_start: 0.8761 (t) cc_final: 0.8500 (t) REVERT: D 423 THR cc_start: 0.8518 (p) cc_final: 0.8293 (t) REVERT: D 545 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8758 (tt) outliers start: 43 outliers final: 19 residues processed: 164 average time/residue: 0.5382 time to fit residues: 98.2285 Evaluate side-chains 149 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 592 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 68 ASN C 211 ASN ** D 506 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 = 0.3311 r_free = 0.3311 target = 0.104197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.087807 restraints weight = 20539.873| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.03 r_work: 0.2902 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13491 Z= 0.235 Angle : 0.662 11.047 18396 Z= 0.331 Chirality : 0.046 0.160 2166 Planarity : 0.005 0.055 2370 Dihedral : 7.324 75.934 1980 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.76 % Allowed : 18.55 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.20), residues: 1732 helix: 0.23 (0.18), residues: 811 sheet: -1.31 (0.40), residues: 179 loop : -1.56 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 8 TYR 0.014 0.001 TYR A 156 PHE 0.014 0.002 PHE B 223 TRP 0.011 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00570 (13487) covalent geometry : angle 0.65210 (18384) hydrogen bonds : bond 0.04681 ( 593) hydrogen bonds : angle 4.74569 ( 1707) metal coordination : bond 0.01150 ( 4) metal coordination : angle 4.56824 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.490 Fit side-chains REVERT: A 222 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: A 300 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8286 (mtp85) REVERT: A 591 ARG cc_start: 0.7872 (ptm-80) cc_final: 0.7582 (tmm-80) REVERT: D 63 GLN cc_start: 0.8373 (tt0) cc_final: 0.7757 (tm-30) REVERT: D 235 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: D 248 MET cc_start: 0.7961 (tpt) cc_final: 0.6511 (tpt) REVERT: D 269 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8244 (pp) REVERT: D 360 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7660 (ptt180) REVERT: D 409 GLU cc_start: 0.8334 (pp20) cc_final: 0.7938 (pp20) REVERT: D 415 SER cc_start: 0.8778 (t) cc_final: 0.8506 (t) REVERT: D 423 THR cc_start: 0.8547 (p) cc_final: 0.8325 (t) REVERT: D 545 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8745 (tt) outliers start: 38 outliers final: 22 residues processed: 161 average time/residue: 0.5330 time to fit residues: 94.7207 Evaluate side-chains 150 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 592 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 24 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 118 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 68 ASN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.088773 restraints weight = 20398.503| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.09 r_work: 0.2934 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13491 Z= 0.124 Angle : 0.594 9.580 18396 Z= 0.295 Chirality : 0.042 0.181 2166 Planarity : 0.004 0.056 2370 Dihedral : 7.065 74.305 1980 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.25 % Allowed : 19.64 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.20), residues: 1732 helix: 0.45 (0.19), residues: 812 sheet: -1.23 (0.38), residues: 192 loop : -1.42 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 8 TYR 0.013 0.001 TYR A 156 PHE 0.010 0.001 PHE A 484 TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00290 (13487) covalent geometry : angle 0.58284 (18384) hydrogen bonds : bond 0.03752 ( 593) hydrogen bonds : angle 4.52800 ( 1707) metal coordination : bond 0.00782 ( 4) metal coordination : angle 4.53342 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.417 Fit side-chains REVERT: A 300 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8208 (mtp85) REVERT: A 591 ARG cc_start: 0.7958 (ptm-80) cc_final: 0.7684 (tmm-80) REVERT: C 36 TYR cc_start: 0.8811 (m-80) cc_final: 0.8465 (m-80) REVERT: C 47 ASP cc_start: 0.8485 (p0) cc_final: 0.8281 (p0) REVERT: D 63 GLN cc_start: 0.8371 (tt0) cc_final: 0.7706 (tm-30) REVERT: D 99 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7684 (tmt) REVERT: D 248 MET cc_start: 0.7867 (tpt) cc_final: 0.6538 (tpt) REVERT: D 269 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8290 (pp) REVERT: D 360 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7550 (ptt180) REVERT: D 409 GLU cc_start: 0.8347 (pp20) cc_final: 0.7925 (pp20) REVERT: D 415 SER cc_start: 0.8743 (t) cc_final: 0.8476 (t) REVERT: D 423 THR cc_start: 0.8383 (p) cc_final: 0.8156 (t) REVERT: D 545 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8700 (tt) outliers start: 31 outliers final: 21 residues processed: 162 average time/residue: 0.5588 time to fit residues: 100.0236 Evaluate side-chains 158 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 583 ASP Chi-restraints excluded: chain D residue 592 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 121 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 149 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.091258 restraints weight = 20439.491| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.06 r_work: 0.2981 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13491 Z= 0.115 Angle : 0.592 9.822 18396 Z= 0.293 Chirality : 0.042 0.164 2166 Planarity : 0.004 0.056 2370 Dihedral : 6.922 72.668 1980 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.11 % Allowed : 20.15 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.20), residues: 1732 helix: 0.59 (0.19), residues: 811 sheet: -1.15 (0.39), residues: 192 loop : -1.38 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 8 TYR 0.013 0.001 TYR A 156 PHE 0.010 0.001 PHE B 223 TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00263 (13487) covalent geometry : angle 0.58143 (18384) hydrogen bonds : bond 0.03513 ( 593) hydrogen bonds : angle 4.41574 ( 1707) metal coordination : bond 0.00589 ( 4) metal coordination : angle 4.40013 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.548 Fit side-chains REVERT: A 300 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8136 (mtp85) REVERT: D 63 GLN cc_start: 0.8372 (tt0) cc_final: 0.7758 (tm-30) REVERT: D 248 MET cc_start: 0.7824 (tpt) cc_final: 0.6581 (tpt) REVERT: D 360 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7566 (ptt180) REVERT: D 409 GLU cc_start: 0.8333 (pp20) cc_final: 0.7906 (pp20) REVERT: D 415 SER cc_start: 0.8706 (t) cc_final: 0.8455 (t) REVERT: D 423 THR cc_start: 0.8399 (p) cc_final: 0.8177 (t) REVERT: D 452 ASP cc_start: 0.8444 (p0) cc_final: 0.8131 (p0) REVERT: D 472 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8363 (tttt) REVERT: D 545 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8721 (tt) outliers start: 29 outliers final: 19 residues processed: 167 average time/residue: 0.5525 time to fit residues: 101.6934 Evaluate side-chains 153 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 590 ASN Chi-restraints excluded: chain D residue 592 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.925 > 50: distance: 44 - 63: 15.013 distance: 54 - 74: 13.087 distance: 58 - 63: 11.249 distance: 63 - 64: 4.150 distance: 64 - 65: 14.113 distance: 64 - 67: 19.569 distance: 65 - 66: 21.549 distance: 65 - 74: 21.750 distance: 67 - 68: 12.694 distance: 68 - 69: 20.981 distance: 69 - 70: 12.058 distance: 70 - 71: 5.391 distance: 71 - 72: 18.931 distance: 71 - 73: 7.617 distance: 74 - 75: 10.909 distance: 75 - 76: 17.914 distance: 75 - 78: 16.924 distance: 76 - 77: 19.679 distance: 76 - 80: 4.907 distance: 78 - 79: 17.521 distance: 79 - 183: 26.167 distance: 80 - 81: 17.302 distance: 80 - 86: 10.092 distance: 81 - 82: 18.758 distance: 81 - 84: 4.168 distance: 82 - 83: 15.715 distance: 82 - 87: 20.112 distance: 84 - 85: 20.135 distance: 85 - 86: 12.264 distance: 87 - 88: 16.949 distance: 88 - 89: 5.673 distance: 88 - 91: 16.998 distance: 89 - 90: 16.864 distance: 89 - 95: 7.208 distance: 91 - 92: 24.614 distance: 92 - 93: 22.145 distance: 92 - 94: 16.402 distance: 95 - 96: 8.651 distance: 96 - 97: 27.135 distance: 96 - 99: 6.220 distance: 97 - 98: 13.208 distance: 97 - 102: 30.777 distance: 99 - 100: 31.998 distance: 99 - 101: 26.892 distance: 102 - 103: 18.539 distance: 103 - 104: 5.559 distance: 103 - 106: 9.385 distance: 104 - 105: 17.484 distance: 104 - 110: 11.193 distance: 106 - 107: 11.512 distance: 106 - 108: 42.353 distance: 110 - 111: 15.741 distance: 111 - 112: 11.695 distance: 111 - 114: 13.342 distance: 112 - 113: 13.054 distance: 112 - 118: 29.538 distance: 113 - 133: 17.109 distance: 114 - 115: 15.920 distance: 115 - 116: 11.717 distance: 115 - 117: 49.720 distance: 118 - 119: 9.633 distance: 119 - 120: 9.560 distance: 119 - 122: 13.335 distance: 120 - 121: 23.248 distance: 120 - 127: 13.131 distance: 121 - 141: 26.425 distance: 122 - 123: 15.761 distance: 123 - 124: 6.163 distance: 124 - 125: 12.390 distance: 124 - 126: 30.842 distance: 127 - 128: 9.666 distance: 128 - 129: 11.015 distance: 128 - 131: 19.318 distance: 129 - 130: 6.493 distance: 129 - 133: 27.206 distance: 131 - 132: 24.843 distance: 132 - 184: 24.501 distance: 133 - 134: 18.313 distance: 134 - 135: 7.889 distance: 134 - 137: 15.250 distance: 135 - 136: 7.029 distance: 135 - 141: 5.511 distance: 137 - 138: 14.029 distance: 138 - 139: 19.906 distance: 138 - 140: 35.211