Starting phenix.real_space_refine on Wed Feb 4 16:53:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rwc_24714/02_2026/7rwc_24714.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rwc_24714/02_2026/7rwc_24714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rwc_24714/02_2026/7rwc_24714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rwc_24714/02_2026/7rwc_24714.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rwc_24714/02_2026/7rwc_24714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rwc_24714/02_2026/7rwc_24714.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.117 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 7857 2.51 5 N 2070 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12110 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4551 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 22, 'TRANS': 590} Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 22, 'TYR:plan': 1, 'ASN:plan1': 4, 'ARG:plan': 6, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 3760 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 26, 'TRANS': 530} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 663 Unresolved non-hydrogen angles: 817 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 35, 'ARG:plan': 8, 'ASP:plan': 29, 'ASN:plan1': 21, 'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 402 Chain: "M" Number of atoms: 2644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2644 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 17, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 540 Unresolved non-hydrogen angles: 646 Unresolved non-hydrogen dihedrals: 453 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 20, 'ARG:plan': 23, 'ASP:plan': 10, 'GLN:plan1': 9, 'ASN:plan1': 8, 'TYR:plan': 2, 'PHE:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 325 Chain: "S" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1115 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 141} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 60 Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.03, per 1000 atoms: 0.25 Number of scatterers: 12110 At special positions: 0 Unit cell: (128.76, 115.44, 108.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 2136 8.00 N 2070 7.00 C 7857 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: 0.96 Conformation dependent library (CDL) restraints added in 718.4 milliseconds 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 10 sheets defined 62.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.663A pdb=" N VAL A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.859A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.749A pdb=" N VAL A 80 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.509A pdb=" N ALA A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 139 removed outlier: 4.009A pdb=" N VAL A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.794A pdb=" N VAL A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 188 through 197 removed outlier: 4.040A pdb=" N ASN A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.891A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.940A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.742A pdb=" N ARG A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.045A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 384 through 397 Processing helix chain 'A' and resid 401 through 415 removed outlier: 3.770A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 6.030A pdb=" N SER A 419 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 420 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 421 " --> pdb=" O TYR A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' Processing helix chain 'A' and resid 422 through 435 Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.960A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.855A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.950A pdb=" N GLN A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 508 through 511 removed outlier: 3.644A pdb=" N ILE A 511 " --> pdb=" O GLY A 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 508 through 511' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.505A pdb=" N GLN A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.982A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 563 Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.544A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.632A pdb=" N ALA A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.522A pdb=" N LEU A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 620 removed outlier: 3.704A pdb=" N ALA A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 62 through 78 removed outlier: 3.655A pdb=" N TYR B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.892A pdb=" N ILE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 4.651A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 3.862A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 149 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.900A pdb=" N GLN B 159 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 removed outlier: 3.725A pdb=" N VAL B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 removed outlier: 3.549A pdb=" N GLU B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 254 through 266 Processing helix chain 'B' and resid 276 through 291 Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 295 through 313 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.616A pdb=" N VAL B 323 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.785A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.515A pdb=" N ARG B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.960A pdb=" N THR B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 470 removed outlier: 3.525A pdb=" N LEU B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 516 through 533 Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.596A pdb=" N LEU B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.768A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 removed outlier: 4.046A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 25 through 38 removed outlier: 3.530A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.572A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 125 through 131 removed outlier: 3.955A pdb=" N THR M 131 " --> pdb=" O GLY M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 383 removed outlier: 3.603A pdb=" N ALA M 382 " --> pdb=" O LYS M 379 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG M 383 " --> pdb=" O LYS M 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 379 through 383' Processing helix chain 'M' and resid 414 through 418 Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.902A pdb=" N GLN S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 118 Processing helix chain 'S' and resid 127 through 137 removed outlier: 3.604A pdb=" N VAL S 131 " --> pdb=" O SER S 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 19 removed outlier: 3.999A pdb=" N ILE M 16 " --> pdb=" O ILE M 7 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL M 68 " --> pdb=" O GLY M 4 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE M 56 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 removed outlier: 3.793A pdb=" N ASP M 117 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 172 through 173 removed outlier: 4.268A pdb=" N GLU M 172 " --> pdb=" O TYR M 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 176 through 185 removed outlier: 3.653A pdb=" N VAL M 201 " --> pdb=" O ASP M 176 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU M 178 " --> pdb=" O ARG M 199 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER M 193 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY M 198 " --> pdb=" O ARG M 276 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG M 276 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL M 200 " --> pdb=" O LEU M 274 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET M 202 " --> pdb=" O PHE M 272 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE M 272 " --> pdb=" O MET M 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 264 through 265 removed outlier: 3.930A pdb=" N PHE M 265 " --> pdb=" O CYS M 212 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS M 212 " --> pdb=" O PHE M 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 289 through 291 removed outlier: 3.574A pdb=" N VAL M 306 " --> pdb=" O ILE M 290 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL M 303 " --> pdb=" O ALA M 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE M 366 " --> pdb=" O VAL M 305 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE M 307 " --> pdb=" O SER M 364 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER M 364 " --> pdb=" O ILE M 307 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN M 334 " --> pdb=" O GLU M 369 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU M 371 " --> pdb=" O GLY M 332 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 341 through 345 removed outlier: 3.669A pdb=" N LYS M 341 " --> pdb=" O LYS M 354 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 341 through 345 removed outlier: 3.669A pdb=" N LYS M 341 " --> pdb=" O LYS M 354 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.998A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU S 16 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2232 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: 1.39 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3895 1.34 - 1.45: 1375 1.45 - 1.57: 6994 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 12334 Sorted by residual: bond pdb=" CA THR A 238 " pdb=" CB THR A 238 " ideal model delta sigma weight residual 1.524 1.547 -0.023 1.62e-02 3.81e+03 2.00e+00 bond pdb=" CB VAL A 483 " pdb=" CG1 VAL A 483 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.69e+00 bond pdb=" CA MET A 10 " pdb=" C MET A 10 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.20e-02 6.94e+03 1.27e+00 bond pdb=" N ILE M 430 " pdb=" CA ILE M 430 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.17e+00 bond pdb=" CB GLU S 82 " pdb=" CG GLU S 82 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 ... (remaining 12329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 16438 1.56 - 3.12: 395 3.12 - 4.68: 51 4.68 - 6.24: 19 6.24 - 7.80: 5 Bond angle restraints: 16908 Sorted by residual: angle pdb=" N VAL B 506 " pdb=" CA VAL B 506 " pdb=" C VAL B 506 " ideal model delta sigma weight residual 113.53 108.45 5.08 9.80e-01 1.04e+00 2.69e+01 angle pdb=" N LEU A 201 " pdb=" CA LEU A 201 " pdb=" C LEU A 201 " ideal model delta sigma weight residual 114.75 109.12 5.63 1.26e+00 6.30e-01 2.00e+01 angle pdb=" N GLU B 501 " pdb=" CA GLU B 501 " pdb=" C GLU B 501 " ideal model delta sigma weight residual 114.16 108.36 5.80 1.48e+00 4.57e-01 1.54e+01 angle pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" O GLN A 199 " ideal model delta sigma weight residual 121.67 117.91 3.76 1.26e+00 6.30e-01 8.91e+00 angle pdb=" N SER A 384 " pdb=" CA SER A 384 " pdb=" C SER A 384 " ideal model delta sigma weight residual 113.88 110.43 3.45 1.23e+00 6.61e-01 7.86e+00 ... (remaining 16903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 6755 17.52 - 35.03: 491 35.03 - 52.55: 81 52.55 - 70.07: 6 70.07 - 87.58: 10 Dihedral angle restraints: 7343 sinusoidal: 2267 harmonic: 5076 Sorted by residual: dihedral pdb=" CA SER A 458 " pdb=" C SER A 458 " pdb=" N GLU A 459 " pdb=" CA GLU A 459 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA GLU A 460 " pdb=" C GLU A 460 " pdb=" N VAL A 461 " pdb=" CA VAL A 461 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN M 74 " pdb=" C ASN M 74 " pdb=" N ALA M 75 " pdb=" CA ALA M 75 " ideal model delta harmonic sigma weight residual -180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 7340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1461 0.038 - 0.075: 511 0.075 - 0.113: 134 0.113 - 0.151: 25 0.151 - 0.188: 3 Chirality restraints: 2134 Sorted by residual: chirality pdb=" CG LEU A 201 " pdb=" CB LEU A 201 " pdb=" CD1 LEU A 201 " pdb=" CD2 LEU A 201 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CB THR A 238 " pdb=" CA THR A 238 " pdb=" OG1 THR A 238 " pdb=" CG2 THR A 238 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 2131 not shown) Planarity restraints: 2134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 268 " 0.061 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO A 269 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 269 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 270 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 22 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C ASN A 22 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN A 22 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS A 23 " 0.008 2.00e-02 2.50e+03 ... (remaining 2131 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 417 2.72 - 3.27: 12578 3.27 - 3.81: 19597 3.81 - 4.36: 21547 4.36 - 4.90: 38183 Nonbonded interactions: 92322 Sorted by model distance: nonbonded pdb=" O LEU B 507 " pdb=" OG1 THR B 511 " model vdw 2.175 3.040 nonbonded pdb=" OG SER M 97 " pdb=" OD1 ASN M 100 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR S 62 " pdb=" ND1 HIS S 85 " model vdw 2.264 3.120 nonbonded pdb=" O PHE M 287 " pdb=" OH TYR M 431 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP A 321 " pdb=" OG SER A 359 " model vdw 2.299 3.040 ... (remaining 92317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.010 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.760 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 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 : 0.004 0.043 12334 Z= 0.159 Angle : 0.605 7.802 16908 Z= 0.334 Chirality : 0.041 0.188 2134 Planarity : 0.004 0.092 2134 Dihedral : 12.871 87.582 4031 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1693 helix: 1.43 (0.17), residues: 966 sheet: -0.16 (0.44), residues: 156 loop : -1.82 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 520 TYR 0.017 0.001 TYR A 463 PHE 0.015 0.001 PHE A 66 TRP 0.014 0.001 TRP A 462 HIS 0.011 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00364 (12334) covalent geometry : angle 0.60481 (16908) hydrogen bonds : bond 0.15245 ( 750) hydrogen bonds : angle 6.19134 ( 2232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7544 (tp) cc_final: 0.6924 (tp) REVERT: A 552 PHE cc_start: 0.7651 (m-80) cc_final: 0.7167 (m-10) REVERT: B 379 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7406 (ttp-170) REVERT: M 187 PRO cc_start: 0.7193 (Cg_exo) cc_final: 0.6852 (Cg_endo) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.0862 time to fit residues: 22.4754 Evaluate side-chains 138 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0770 chunk 149 optimal weight: 20.0000 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 200 HIS ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.233038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.206716 restraints weight = 14081.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.205847 restraints weight = 16589.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.205905 restraints weight = 16856.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.206035 restraints weight = 14792.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.206063 restraints weight = 14604.287| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12334 Z= 0.142 Angle : 0.543 7.317 16908 Z= 0.286 Chirality : 0.041 0.195 2134 Planarity : 0.004 0.071 2134 Dihedral : 3.970 28.514 1818 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.67 % Allowed : 9.53 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1693 helix: 1.38 (0.17), residues: 981 sheet: -0.15 (0.46), residues: 154 loop : -1.78 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 379 TYR 0.013 0.001 TYR A 247 PHE 0.018 0.002 PHE S 55 TRP 0.016 0.001 TRP B 527 HIS 0.004 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00333 (12334) covalent geometry : angle 0.54301 (16908) hydrogen bonds : bond 0.04054 ( 750) hydrogen bonds : angle 4.64063 ( 2232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7339 (tp) cc_final: 0.7074 (tp) REVERT: M 162 ARG cc_start: 0.4701 (ptt180) cc_final: 0.3759 (mpp80) REVERT: M 187 PRO cc_start: 0.7820 (Cg_exo) cc_final: 0.7568 (Cg_endo) REVERT: M 216 MET cc_start: 0.6776 (ppp) cc_final: 0.5949 (ppp) REVERT: M 425 ILE cc_start: 0.8585 (mm) cc_final: 0.8296 (mm) outliers start: 18 outliers final: 8 residues processed: 168 average time/residue: 0.0840 time to fit residues: 21.5937 Evaluate side-chains 152 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 158 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.230258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.220636 restraints weight = 14260.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.197959 restraints weight = 25198.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.198396 restraints weight = 21446.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.198731 restraints weight = 19703.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.200002 restraints weight = 15559.310| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12334 Z= 0.159 Angle : 0.538 7.003 16908 Z= 0.285 Chirality : 0.041 0.198 2134 Planarity : 0.004 0.064 2134 Dihedral : 3.879 20.255 1816 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.41 % Allowed : 12.58 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1693 helix: 1.39 (0.17), residues: 977 sheet: -0.28 (0.45), residues: 154 loop : -1.80 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 579 TYR 0.013 0.001 TYR A 418 PHE 0.016 0.001 PHE A 66 TRP 0.015 0.001 TRP A 462 HIS 0.004 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00388 (12334) covalent geometry : angle 0.53762 (16908) hydrogen bonds : bond 0.03951 ( 750) hydrogen bonds : angle 4.41298 ( 2232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: M 77 MET cc_start: 0.7785 (ttp) cc_final: 0.7181 (ttp) REVERT: M 162 ARG cc_start: 0.5243 (ptt180) cc_final: 0.4310 (mpp80) REVERT: M 216 MET cc_start: 0.6854 (ppp) cc_final: 0.5741 (ppp) outliers start: 26 outliers final: 20 residues processed: 165 average time/residue: 0.0791 time to fit residues: 20.5096 Evaluate side-chains 161 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 305 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain M residue 349 ASN Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 44 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 218 ASN M 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.231428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.221612 restraints weight = 14224.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.199889 restraints weight = 26201.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.199668 restraints weight = 24513.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.200489 restraints weight = 22097.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.200760 restraints weight = 16881.972| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12334 Z= 0.131 Angle : 0.506 6.641 16908 Z= 0.269 Chirality : 0.041 0.230 2134 Planarity : 0.004 0.059 2134 Dihedral : 3.810 19.803 1816 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.24 % Allowed : 14.06 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1693 helix: 1.51 (0.17), residues: 978 sheet: -0.37 (0.45), residues: 154 loop : -1.78 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 42 TYR 0.018 0.001 TYR A 88 PHE 0.014 0.001 PHE A 66 TRP 0.016 0.001 TRP A 462 HIS 0.005 0.001 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00311 (12334) covalent geometry : angle 0.50649 (16908) hydrogen bonds : bond 0.03666 ( 750) hydrogen bonds : angle 4.21760 ( 2232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 551 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7541 (tt) REVERT: B 208 LEU cc_start: 0.6519 (mm) cc_final: 0.5858 (tp) REVERT: B 399 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8026 (tt) REVERT: B 562 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8049 (tm-30) REVERT: M 77 MET cc_start: 0.7778 (ttp) cc_final: 0.7131 (ttp) REVERT: M 162 ARG cc_start: 0.5093 (ptt180) cc_final: 0.3987 (mpp80) REVERT: M 216 MET cc_start: 0.6835 (ppp) cc_final: 0.5715 (ppp) outliers start: 35 outliers final: 24 residues processed: 179 average time/residue: 0.0831 time to fit residues: 23.0600 Evaluate side-chains 172 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 305 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 32 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 chunk 164 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 110 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.232187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.222566 restraints weight = 14177.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.202124 restraints weight = 23795.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.201155 restraints weight = 23192.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.201704 restraints weight = 20139.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.202545 restraints weight = 16103.903| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12334 Z= 0.123 Angle : 0.497 6.633 16908 Z= 0.264 Chirality : 0.040 0.202 2134 Planarity : 0.004 0.056 2134 Dihedral : 3.739 19.390 1816 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 3.33 % Allowed : 15.63 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1693 helix: 1.57 (0.17), residues: 979 sheet: -0.35 (0.45), residues: 154 loop : -1.79 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 42 TYR 0.014 0.001 TYR A 418 PHE 0.014 0.001 PHE S 55 TRP 0.016 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00291 (12334) covalent geometry : angle 0.49696 (16908) hydrogen bonds : bond 0.03517 ( 750) hydrogen bonds : angle 4.10351 ( 2232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 249 TYR cc_start: 0.8423 (t80) cc_final: 0.7998 (t80) REVERT: A 551 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7571 (tt) REVERT: A 577 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.6711 (tt0) REVERT: B 562 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8072 (tm-30) REVERT: M 1 MET cc_start: 0.7649 (ptp) cc_final: 0.7333 (mtm) REVERT: M 162 ARG cc_start: 0.5246 (ptt180) cc_final: 0.4156 (mpp80) REVERT: M 216 MET cc_start: 0.6815 (ppp) cc_final: 0.5707 (ppp) outliers start: 36 outliers final: 23 residues processed: 182 average time/residue: 0.0814 time to fit residues: 22.9386 Evaluate side-chains 179 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 108 optimal weight: 0.0670 chunk 155 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 chunk 159 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 20.0000 chunk 141 optimal weight: 0.1980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN M 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.232675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.223402 restraints weight = 14155.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.206380 restraints weight = 27442.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.202726 restraints weight = 26018.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.203330 restraints weight = 21333.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.204256 restraints weight = 16440.618| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12334 Z= 0.117 Angle : 0.496 7.626 16908 Z= 0.262 Chirality : 0.040 0.215 2134 Planarity : 0.003 0.054 2134 Dihedral : 3.661 19.316 1816 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 3.42 % Allowed : 17.02 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1693 helix: 1.62 (0.17), residues: 983 sheet: -0.37 (0.45), residues: 154 loop : -1.79 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 3 TYR 0.015 0.001 TYR A 418 PHE 0.015 0.001 PHE S 55 TRP 0.017 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00273 (12334) covalent geometry : angle 0.49575 (16908) hydrogen bonds : bond 0.03383 ( 750) hydrogen bonds : angle 4.01861 ( 2232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 249 TYR cc_start: 0.8374 (t80) cc_final: 0.8028 (t80) REVERT: A 577 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.6712 (tt0) REVERT: B 208 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6155 (tp) REVERT: B 562 GLU cc_start: 0.8802 (tm-30) cc_final: 0.7975 (tm-30) REVERT: M 1 MET cc_start: 0.7660 (ptp) cc_final: 0.7324 (mtm) REVERT: M 162 ARG cc_start: 0.5231 (ptt180) cc_final: 0.4295 (mpp80) REVERT: M 216 MET cc_start: 0.6471 (ppp) cc_final: 0.5400 (ppp) outliers start: 37 outliers final: 23 residues processed: 181 average time/residue: 0.0823 time to fit residues: 23.1974 Evaluate side-chains 173 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 135 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 19 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 91 optimal weight: 0.0570 chunk 78 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.230889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.221641 restraints weight = 14127.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.204459 restraints weight = 28817.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.201922 restraints weight = 23347.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.202213 restraints weight = 20063.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.202754 restraints weight = 15500.566| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12334 Z= 0.135 Angle : 0.519 7.219 16908 Z= 0.271 Chirality : 0.041 0.245 2134 Planarity : 0.004 0.053 2134 Dihedral : 3.697 17.702 1816 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 3.24 % Allowed : 17.67 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1693 helix: 1.60 (0.17), residues: 981 sheet: -0.33 (0.45), residues: 154 loop : -1.81 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 313 TYR 0.013 0.001 TYR A 88 PHE 0.014 0.001 PHE S 55 TRP 0.013 0.001 TRP A 462 HIS 0.003 0.001 HIS S 36 Details of bonding type rmsd covalent geometry : bond 0.00328 (12334) covalent geometry : angle 0.51892 (16908) hydrogen bonds : bond 0.03507 ( 750) hydrogen bonds : angle 4.01032 ( 2232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 TYR cc_start: 0.8371 (t80) cc_final: 0.7957 (t80) REVERT: A 577 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.6785 (tt0) REVERT: B 208 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.5998 (tp) REVERT: B 313 ARG cc_start: 0.7683 (tpp80) cc_final: 0.7239 (tpp-160) REVERT: B 562 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8034 (tm-30) REVERT: M 1 MET cc_start: 0.7705 (ptp) cc_final: 0.7370 (mtm) REVERT: M 162 ARG cc_start: 0.5342 (ptt180) cc_final: 0.4312 (mpp80) REVERT: M 216 MET cc_start: 0.6573 (ppp) cc_final: 0.5600 (ppp) REVERT: M 425 ILE cc_start: 0.8635 (mt) cc_final: 0.8384 (mt) outliers start: 35 outliers final: 26 residues processed: 182 average time/residue: 0.0874 time to fit residues: 24.5257 Evaluate side-chains 180 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 135 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 3 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 159 optimal weight: 0.0970 chunk 74 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.230939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.221621 restraints weight = 14135.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.204166 restraints weight = 29774.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.201372 restraints weight = 23719.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.202412 restraints weight = 18668.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.202968 restraints weight = 15116.215| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12334 Z= 0.133 Angle : 0.516 6.676 16908 Z= 0.271 Chirality : 0.041 0.247 2134 Planarity : 0.004 0.052 2134 Dihedral : 3.698 18.140 1816 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 3.52 % Allowed : 18.32 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1693 helix: 1.62 (0.17), residues: 981 sheet: -0.32 (0.45), residues: 154 loop : -1.83 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 313 TYR 0.016 0.001 TYR A 418 PHE 0.027 0.001 PHE S 55 TRP 0.015 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00322 (12334) covalent geometry : angle 0.51630 (16908) hydrogen bonds : bond 0.03508 ( 750) hydrogen bonds : angle 4.00071 ( 2232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 249 TYR cc_start: 0.8357 (t80) cc_final: 0.7931 (t80) REVERT: A 577 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.6777 (tt0) REVERT: B 208 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6019 (tp) REVERT: B 313 ARG cc_start: 0.7689 (tpp80) cc_final: 0.7251 (tpp-160) REVERT: B 562 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8003 (tm-30) REVERT: M 1 MET cc_start: 0.7648 (ptp) cc_final: 0.7398 (mtm) REVERT: M 162 ARG cc_start: 0.5446 (ptt180) cc_final: 0.4400 (mpp80) REVERT: M 216 MET cc_start: 0.6567 (ppp) cc_final: 0.5555 (ppp) REVERT: M 425 ILE cc_start: 0.8640 (mt) cc_final: 0.8392 (mt) outliers start: 38 outliers final: 29 residues processed: 183 average time/residue: 0.0840 time to fit residues: 23.8472 Evaluate side-chains 183 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 305 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain S residue 135 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 161 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.0000 chunk 142 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 140 optimal weight: 0.0270 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.0470 chunk 98 optimal weight: 0.9990 overall best weight: 0.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.233789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.225015 restraints weight = 14071.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.208353 restraints weight = 28776.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.206079 restraints weight = 30702.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.206126 restraints weight = 24981.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.206899 restraints weight = 18388.451| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12334 Z= 0.109 Angle : 0.498 6.829 16908 Z= 0.262 Chirality : 0.040 0.239 2134 Planarity : 0.003 0.051 2134 Dihedral : 3.604 17.721 1816 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 2.78 % Allowed : 19.80 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1693 helix: 1.74 (0.17), residues: 984 sheet: -0.32 (0.45), residues: 152 loop : -1.82 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 313 TYR 0.012 0.001 TYR A 88 PHE 0.028 0.001 PHE A 66 TRP 0.020 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00251 (12334) covalent geometry : angle 0.49793 (16908) hydrogen bonds : bond 0.03257 ( 750) hydrogen bonds : angle 3.90765 ( 2232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: B 208 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6073 (tp) REVERT: B 313 ARG cc_start: 0.7683 (tpp80) cc_final: 0.7277 (tpp-160) REVERT: B 562 GLU cc_start: 0.8718 (tm-30) cc_final: 0.7963 (tm-30) REVERT: M 1 MET cc_start: 0.7550 (ptp) cc_final: 0.7283 (mtm) REVERT: M 162 ARG cc_start: 0.5237 (ptt180) cc_final: 0.4190 (mpp80) REVERT: M 216 MET cc_start: 0.6394 (ppp) cc_final: 0.5496 (ppp) REVERT: M 425 ILE cc_start: 0.8601 (mt) cc_final: 0.8340 (mt) outliers start: 30 outliers final: 23 residues processed: 176 average time/residue: 0.0793 time to fit residues: 21.7639 Evaluate side-chains 172 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.230693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.221474 restraints weight = 14151.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.203028 restraints weight = 29760.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.201684 restraints weight = 24521.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.202117 restraints weight = 18950.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.202556 restraints weight = 15816.864| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12334 Z= 0.137 Angle : 0.530 9.216 16908 Z= 0.276 Chirality : 0.041 0.245 2134 Planarity : 0.004 0.052 2134 Dihedral : 3.660 18.273 1816 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 2.78 % Allowed : 19.98 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1693 helix: 1.67 (0.17), residues: 983 sheet: -0.33 (0.45), residues: 152 loop : -1.81 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 313 TYR 0.014 0.001 TYR A 418 PHE 0.026 0.001 PHE A 66 TRP 0.013 0.001 TRP M 353 HIS 0.003 0.001 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00332 (12334) covalent geometry : angle 0.52992 (16908) hydrogen bonds : bond 0.03484 ( 750) hydrogen bonds : angle 3.95129 ( 2232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 577 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.6769 (tt0) REVERT: B 208 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6038 (tp) REVERT: B 313 ARG cc_start: 0.7705 (tpp80) cc_final: 0.7304 (tpp-160) REVERT: B 562 GLU cc_start: 0.8719 (tm-30) cc_final: 0.7932 (tm-30) REVERT: M 1 MET cc_start: 0.7682 (ptp) cc_final: 0.7373 (mtm) REVERT: M 162 ARG cc_start: 0.5512 (ptt180) cc_final: 0.4438 (mpp80) REVERT: M 216 MET cc_start: 0.6490 (ppp) cc_final: 0.5478 (ppp) REVERT: M 425 ILE cc_start: 0.8612 (mt) cc_final: 0.8361 (mt) outliers start: 30 outliers final: 25 residues processed: 172 average time/residue: 0.0829 time to fit residues: 22.2577 Evaluate side-chains 173 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 40 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 137 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.230602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.221723 restraints weight = 14096.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.204573 restraints weight = 26967.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.201849 restraints weight = 22900.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.201891 restraints weight = 20237.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.202815 restraints weight = 15656.745| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12334 Z= 0.136 Angle : 0.538 15.135 16908 Z= 0.278 Chirality : 0.041 0.246 2134 Planarity : 0.004 0.051 2134 Dihedral : 3.674 18.032 1816 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 3.05 % Allowed : 20.17 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1693 helix: 1.62 (0.17), residues: 989 sheet: -0.31 (0.45), residues: 152 loop : -1.83 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 313 TYR 0.013 0.001 TYR A 418 PHE 0.025 0.001 PHE A 66 TRP 0.014 0.001 TRP A 462 HIS 0.003 0.001 HIS S 36 Details of bonding type rmsd covalent geometry : bond 0.00330 (12334) covalent geometry : angle 0.53809 (16908) hydrogen bonds : bond 0.03476 ( 750) hydrogen bonds : angle 3.94180 ( 2232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1554.65 seconds wall clock time: 27 minutes 43.97 seconds (1663.97 seconds total)