Starting phenix.real_space_refine on Thu Jul 31 05:18:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5t_35993/07_2025/8j5t_35993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5t_35993/07_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_35993/07_2025/8j5t_35993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5t_35993/07_2025/8j5t_35993.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5t_35993/07_2025/8j5t_35993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5t_35993/07_2025/8j5t_35993.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.74, per 1000 atoms: 0.66 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: 3.83 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.81 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: 4.51 Time building geometry restraints manager: 4.52 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 38.450 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.020 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (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 TRP 0.013 0.002 TRP A 339 HIS 0.013 0.001 HIS C 62 PHE 0.018 0.002 PHE A 440 TYR 0.017 0.002 TYR A 441 ARG 0.013 0.001 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.18089 ( 593) hydrogen bonds : angle 7.39174 ( 1707) metal coordination : bond 0.03084 ( 4) metal coordination : angle 0.02458 ( 12) covalent geometry : bond 0.00730 (13487) covalent geometry : angle 0.96159 (18384) *********************** 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 : 1.425 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: 1.2157 time to fit residues: 220.5400 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 : 1.416 ------------------------------------------------------------------------------- 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 144 optimal weight: 0.0670 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.106643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.090056 restraints weight = 20396.437| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.06 r_work: 0.3012 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13491 Z= 0.145 Angle : 0.648 10.852 18396 Z= 0.331 Chirality : 0.044 0.159 2166 Planarity : 0.005 0.059 2370 Dihedral : 8.518 107.958 1985 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.89 % Allowed : 10.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.19), residues: 1732 helix: -0.40 (0.18), residues: 811 sheet: -1.64 (0.39), residues: 172 loop : -1.66 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 119 HIS 0.008 0.001 HIS C 62 PHE 0.010 0.001 PHE D 151 TYR 0.013 0.001 TYR A 156 ARG 0.007 0.001 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.04884 ( 593) hydrogen bonds : angle 5.26152 ( 1707) metal coordination : bond 0.00921 ( 4) metal coordination : angle 3.79873 ( 12) covalent geometry : bond 0.00332 (13487) covalent geometry : angle 0.64124 (18384) *********************** 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 170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.450 Fit side-chains REVERT: A 442 ASP cc_start: 0.8048 (t0) cc_final: 0.7467 (t70) REVERT: B 95 ILE cc_start: 0.8624 (pt) cc_final: 0.8418 (mt) REVERT: C 47 ASP cc_start: 0.8510 (p0) cc_final: 0.8195 (p0) REVERT: D 63 GLN cc_start: 0.8367 (tt0) cc_final: 0.7795 (tm-30) REVERT: D 65 ARG cc_start: 0.8545 (ttp80) cc_final: 0.8155 (ttp80) REVERT: D 248 MET cc_start: 0.7708 (tpt) cc_final: 0.6671 (tpt) REVERT: D 269 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8336 (pp) REVERT: D 360 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7529 (ptt180) REVERT: D 409 GLU cc_start: 0.8317 (pp20) cc_final: 0.7937 (pp20) REVERT: D 423 THR cc_start: 0.8710 (p) cc_final: 0.8479 (t) outliers start: 26 outliers final: 8 residues processed: 157 average time/residue: 1.1504 time to fit residues: 200.2028 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 : 1.550 ------------------------------------------------------------------------------- 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 C residue 2 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 583 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 138 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN B 39 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.102769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.086000 restraints weight = 20652.630| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.08 r_work: 0.2875 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 13491 Z= 0.260 Angle : 0.693 10.273 18396 Z= 0.351 Chirality : 0.047 0.166 2166 Planarity : 0.005 0.059 2370 Dihedral : 7.900 76.883 1980 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.05 % Allowed : 15.05 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1732 helix: -0.19 (0.18), residues: 811 sheet: -1.51 (0.39), residues: 178 loop : -1.76 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 339 HIS 0.006 0.001 HIS C 62 PHE 0.016 0.002 PHE B 272 TYR 0.015 0.002 TYR A 156 ARG 0.004 0.001 ARG D 597 Details of bonding type rmsd hydrogen bonds : bond 0.05282 ( 593) hydrogen bonds : angle 5.10627 ( 1707) metal coordination : bond 0.01403 ( 4) metal coordination : angle 4.54910 ( 12) covalent geometry : bond 0.00627 (13487) covalent geometry : angle 0.68292 (18384) *********************** 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 169 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 1.541 Fit side-chains REVERT: B 279 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7960 (tt0) REVERT: C 47 ASP cc_start: 0.8581 (p0) cc_final: 0.8334 (p0) REVERT: C 233 ASP cc_start: 0.8231 (p0) cc_final: 0.7929 (p0) REVERT: D 63 GLN cc_start: 0.8363 (tt0) cc_final: 0.7759 (tm-30) REVERT: D 99 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7674 (tmt) REVERT: D 235 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: D 260 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7659 (ttm110) REVERT: D 269 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8335 (pp) REVERT: D 360 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7653 (ptt180) REVERT: D 409 GLU cc_start: 0.8330 (pp20) cc_final: 0.7874 (pp20) REVERT: D 423 THR cc_start: 0.8672 (p) cc_final: 0.8421 (t) outliers start: 42 outliers final: 17 residues processed: 157 average time/residue: 1.3039 time to fit residues: 228.6545 Evaluate side-chains 142 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL 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 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 273 ASP 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 178 CYS 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 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 74 optimal weight: 0.0870 chunk 119 optimal weight: 0.5980 chunk 54 optimal weight: 0.0980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 68 ASN B 191 HIS C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.091745 restraints weight = 20193.860| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.05 r_work: 0.2996 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13491 Z= 0.109 Angle : 0.581 9.451 18396 Z= 0.291 Chirality : 0.041 0.137 2166 Planarity : 0.004 0.056 2370 Dihedral : 7.252 68.689 1980 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.04 % Allowed : 16.95 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1732 helix: 0.24 (0.19), residues: 810 sheet: -1.25 (0.40), residues: 186 loop : -1.51 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 119 HIS 0.004 0.001 HIS C 62 PHE 0.009 0.001 PHE B 223 TYR 0.012 0.001 TYR A 156 ARG 0.009 0.001 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 593) hydrogen bonds : angle 4.60495 ( 1707) metal coordination : bond 0.00704 ( 4) metal coordination : angle 4.56408 ( 12) covalent geometry : bond 0.00242 (13487) covalent geometry : angle 0.56978 (18384) *********************** 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 173 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 2.198 Fit side-chains REVERT: B 189 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9020 (mm) REVERT: C 47 ASP cc_start: 0.8472 (p0) cc_final: 0.8226 (p0) REVERT: C 147 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6606 (mmp) REVERT: D 63 GLN cc_start: 0.8350 (tt0) cc_final: 0.7764 (tm-30) REVERT: D 65 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7852 (ttp80) REVERT: D 269 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8294 (pp) REVERT: D 360 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7519 (ptt180) REVERT: D 409 GLU cc_start: 0.8306 (pp20) cc_final: 0.7928 (pp20) REVERT: D 452 ASP cc_start: 0.8387 (p0) cc_final: 0.8119 (p0) outliers start: 28 outliers final: 9 residues processed: 165 average time/residue: 1.3902 time to fit residues: 253.3291 Evaluate side-chains 142 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 LEU Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 204 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 556 VAL Chi-restraints excluded: chain D residue 583 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 20 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 chunk 120 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.104950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.088204 restraints weight = 20486.997| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.07 r_work: 0.2925 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13491 Z= 0.195 Angle : 0.621 10.013 18396 Z= 0.312 Chirality : 0.044 0.152 2166 Planarity : 0.004 0.055 2370 Dihedral : 7.269 73.097 1980 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.76 % Allowed : 17.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.20), residues: 1732 helix: 0.26 (0.19), residues: 810 sheet: -1.27 (0.40), residues: 179 loop : -1.59 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 PHE 0.013 0.001 PHE C 177 TYR 0.014 0.001 TYR A 156 ARG 0.010 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 593) hydrogen bonds : angle 4.67535 ( 1707) metal coordination : bond 0.01024 ( 4) metal coordination : angle 4.31602 ( 12) covalent geometry : bond 0.00471 (13487) covalent geometry : angle 0.61118 (18384) *********************** 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 165 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.518 Fit side-chains REVERT: A 331 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8966 (mt) REVERT: C 47 ASP cc_start: 0.8548 (p0) cc_final: 0.8317 (p0) REVERT: D 63 GLN cc_start: 0.8380 (tt0) cc_final: 0.7733 (tm-30) REVERT: D 65 ARG cc_start: 0.8461 (ttp80) cc_final: 0.7923 (ttp80) REVERT: D 99 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7718 (tmt) REVERT: D 269 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8348 (pp) REVERT: D 360 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7616 (ptt180) REVERT: D 409 GLU cc_start: 0.8349 (pp20) cc_final: 0.7951 (pp20) REVERT: D 415 SER cc_start: 0.8762 (t) cc_final: 0.8496 (t) REVERT: D 452 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8205 (p0) outliers start: 38 outliers final: 15 residues processed: 158 average time/residue: 1.0163 time to fit residues: 179.4391 Evaluate side-chains 142 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 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 D residue 93 THR Chi-restraints excluded: chain D residue 99 MET 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 452 ASP Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 117 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.089139 restraints weight = 20536.150| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.05 r_work: 0.2924 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13491 Z= 0.189 Angle : 0.621 9.477 18396 Z= 0.313 Chirality : 0.044 0.148 2166 Planarity : 0.005 0.055 2370 Dihedral : 7.265 76.196 1980 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.13 % Allowed : 18.33 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1732 helix: 0.28 (0.18), residues: 811 sheet: -1.30 (0.40), residues: 179 loop : -1.58 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 PHE 0.012 0.001 PHE B 223 TYR 0.013 0.001 TYR A 156 ARG 0.010 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 593) hydrogen bonds : angle 4.67101 ( 1707) metal coordination : bond 0.01107 ( 4) metal coordination : angle 4.47004 ( 12) covalent geometry : bond 0.00455 (13487) covalent geometry : angle 0.61092 (18384) *********************** 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 172 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 1.987 Fit side-chains REVERT: C 47 ASP cc_start: 0.8575 (p0) cc_final: 0.8345 (p0) REVERT: D 63 GLN cc_start: 0.8382 (tt0) cc_final: 0.7766 (tm-30) REVERT: D 269 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8384 (pp) REVERT: D 360 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7622 (ptt180) REVERT: D 409 GLU cc_start: 0.8355 (pp20) cc_final: 0.7969 (pp20) REVERT: D 415 SER cc_start: 0.8758 (t) cc_final: 0.8486 (t) REVERT: D 452 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8202 (p0) REVERT: D 545 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8716 (tt) outliers start: 43 outliers final: 19 residues processed: 165 average time/residue: 1.7835 time to fit residues: 328.9454 Evaluate side-chains 149 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 80 THR 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 C residue 84 SER 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 213 HIS 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 452 ASP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.104069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.087299 restraints weight = 20650.994| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.09 r_work: 0.2908 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13491 Z= 0.203 Angle : 0.633 9.876 18396 Z= 0.318 Chirality : 0.044 0.161 2166 Planarity : 0.005 0.055 2370 Dihedral : 7.274 79.931 1980 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.35 % Allowed : 18.33 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1732 helix: 0.28 (0.18), residues: 812 sheet: -1.27 (0.40), residues: 179 loop : -1.57 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 339 HIS 0.003 0.001 HIS C 62 PHE 0.012 0.001 PHE B 223 TYR 0.013 0.001 TYR A 156 ARG 0.010 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 593) hydrogen bonds : angle 4.67950 ( 1707) metal coordination : bond 0.00999 ( 4) metal coordination : angle 4.52991 ( 12) covalent geometry : bond 0.00488 (13487) covalent geometry : angle 0.62289 (18384) *********************** 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 177 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 2.841 Fit side-chains REVERT: A 520 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: A 591 ARG cc_start: 0.7944 (ptm-80) cc_final: 0.7659 (tmm-80) REVERT: B 99 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8629 (tp) REVERT: D 63 GLN cc_start: 0.8389 (tt0) cc_final: 0.7728 (tm-30) REVERT: D 99 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7751 (tmt) REVERT: D 235 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: D 269 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8355 (pp) REVERT: D 360 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7641 (ptt180) REVERT: D 409 GLU cc_start: 0.8373 (pp20) cc_final: 0.7954 (pp20) REVERT: D 415 SER cc_start: 0.8769 (t) cc_final: 0.8493 (t) REVERT: D 452 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8225 (p0) REVERT: D 545 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8707 (tt) outliers start: 46 outliers final: 21 residues processed: 169 average time/residue: 1.4932 time to fit residues: 281.2897 Evaluate side-chains 154 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 A residue 520 GLN Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 99 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 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 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 452 ASP 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 587 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 112 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.105072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.088575 restraints weight = 20529.048| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.09 r_work: 0.2935 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13491 Z= 0.121 Angle : 0.598 9.638 18396 Z= 0.298 Chirality : 0.042 0.176 2166 Planarity : 0.004 0.055 2370 Dihedral : 7.082 78.594 1980 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.33 % Allowed : 20.07 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1732 helix: 0.46 (0.19), residues: 813 sheet: -1.20 (0.39), residues: 192 loop : -1.41 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.003 0.001 HIS B 241 PHE 0.010 0.001 PHE A 484 TYR 0.012 0.001 TYR A 156 ARG 0.011 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 593) hydrogen bonds : angle 4.51635 ( 1707) metal coordination : bond 0.00669 ( 4) metal coordination : angle 4.39061 ( 12) covalent geometry : bond 0.00280 (13487) covalent geometry : angle 0.58710 (18384) *********************** 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 169 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.604 Fit side-chains REVERT: A 591 ARG cc_start: 0.7878 (ptm-80) cc_final: 0.7667 (tmm-80) REVERT: D 63 GLN cc_start: 0.8382 (tt0) cc_final: 0.7724 (tm-30) REVERT: D 360 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7554 (ptt180) REVERT: D 409 GLU cc_start: 0.8419 (pp20) cc_final: 0.7972 (pp20) REVERT: D 415 SER cc_start: 0.8737 (t) cc_final: 0.8466 (t) REVERT: D 545 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8693 (tt) outliers start: 32 outliers final: 22 residues processed: 166 average time/residue: 1.0187 time to fit residues: 188.4423 Evaluate side-chains 152 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 135 LEU 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 C residue 84 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 251 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 29 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 138 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 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 = 0.3296 r_free = 0.3296 target = 0.104243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.087512 restraints weight = 20533.604| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.11 r_work: 0.2914 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13491 Z= 0.164 Angle : 0.618 9.913 18396 Z= 0.310 Chirality : 0.043 0.161 2166 Planarity : 0.005 0.056 2370 Dihedral : 7.077 79.798 1980 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.40 % Allowed : 20.65 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1732 helix: 0.46 (0.19), residues: 814 sheet: -1.15 (0.38), residues: 193 loop : -1.45 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.003 0.001 HIS C 62 PHE 0.012 0.001 PHE B 223 TYR 0.013 0.001 TYR A 156 ARG 0.010 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 593) hydrogen bonds : angle 4.54981 ( 1707) metal coordination : bond 0.00887 ( 4) metal coordination : angle 4.27136 ( 12) covalent geometry : bond 0.00392 (13487) covalent geometry : angle 0.60864 (18384) *********************** 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 168 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.436 Fit side-chains REVERT: D 63 GLN cc_start: 0.8403 (tt0) cc_final: 0.7747 (tm-30) REVERT: D 99 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7749 (tmt) REVERT: D 235 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: D 360 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7579 (ptt180) REVERT: D 409 GLU cc_start: 0.8420 (pp20) cc_final: 0.7982 (pp20) REVERT: D 415 SER cc_start: 0.8756 (t) cc_final: 0.8489 (t) REVERT: D 472 LYS cc_start: 0.8754 (ptpp) cc_final: 0.8185 (ttpp) REVERT: D 545 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8709 (tt) outliers start: 33 outliers final: 26 residues processed: 166 average time/residue: 1.0028 time to fit residues: 186.3401 Evaluate side-chains 161 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 379 THR 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 144 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 68 VAL 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 234 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 386 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 111 optimal weight: 0.0770 chunk 160 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 0.0060 chunk 68 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 249 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.092047 restraints weight = 20279.962| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.04 r_work: 0.2994 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13491 Z= 0.110 Angle : 0.591 9.508 18396 Z= 0.295 Chirality : 0.041 0.154 2166 Planarity : 0.004 0.058 2370 Dihedral : 6.917 76.448 1980 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.89 % Allowed : 21.60 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1732 helix: 0.65 (0.19), residues: 814 sheet: -1.06 (0.39), residues: 190 loop : -1.36 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS B 241 PHE 0.009 0.001 PHE D 555 TYR 0.013 0.001 TYR A 156 ARG 0.013 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 593) hydrogen bonds : angle 4.39405 ( 1707) metal coordination : bond 0.00572 ( 4) metal coordination : angle 4.56430 ( 12) covalent geometry : bond 0.00248 (13487) covalent geometry : angle 0.57960 (18384) ********************** REFINEMENT MACRO_CYCLE 10 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: 26 poor density : 140 time to evaluate : 1.517 Fit side-chains REVERT: B 271 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8987 (tp) REVERT: C 36 TYR cc_start: 0.8658 (m-80) cc_final: 0.8456 (m-80) REVERT: D 63 GLN cc_start: 0.8390 (tt0) cc_final: 0.7760 (tm-30) REVERT: D 360 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7566 (ptt180) REVERT: D 409 GLU cc_start: 0.8365 (pp20) cc_final: 0.7935 (pp20) REVERT: D 415 SER cc_start: 0.8718 (t) cc_final: 0.8452 (t) REVERT: D 452 ASP cc_start: 0.8444 (p0) cc_final: 0.8169 (p0) REVERT: D 472 LYS cc_start: 0.8748 (ptpp) cc_final: 0.8224 (ttpp) REVERT: D 545 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8678 (tt) outliers start: 26 outliers final: 16 residues processed: 163 average time/residue: 1.0259 time to fit residues: 186.8333 Evaluate side-chains 147 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 THR 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 B residue 271 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 251 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 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 583 ASP Chi-restraints excluded: chain D residue 590 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 59 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 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 = 0.3356 r_free = 0.3356 target = 0.107709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.091308 restraints weight = 20603.378| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.07 r_work: 0.2985 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2477 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= 0.122 Angle : 0.605 10.091 18396 Z= 0.300 Chirality : 0.042 0.144 2166 Planarity : 0.004 0.058 2370 Dihedral : 6.853 75.516 1980 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.96 % Allowed : 22.04 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1732 helix: 0.71 (0.19), residues: 813 sheet: -1.09 (0.39), residues: 192 loop : -1.34 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS B 241 PHE 0.010 0.001 PHE D 555 TYR 0.013 0.001 TYR A 156 ARG 0.011 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 593) hydrogen bonds : angle 4.38002 ( 1707) metal coordination : bond 0.00763 ( 4) metal coordination : angle 4.44829 ( 12) covalent geometry : bond 0.00284 (13487) covalent geometry : angle 0.59474 (18384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8957.74 seconds wall clock time: 160 minutes 49.42 seconds (9649.42 seconds total)