Starting phenix.real_space_refine on Fri Sep 19 04:46:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kzt_62668/09_2025/9kzt_62668_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kzt_62668/09_2025/9kzt_62668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kzt_62668/09_2025/9kzt_62668_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kzt_62668/09_2025/9kzt_62668_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kzt_62668/09_2025/9kzt_62668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kzt_62668/09_2025/9kzt_62668.map" } resolution = 3.79 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= -0.001 sd= 0.015 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 198 5.16 5 C 14859 2.51 5 N 3978 2.21 5 O 4491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23526 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3696 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 13, 'TRANS': 468} Chain breaks: 1 Chain: "B" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4146 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 20, 'TRANS': 490} Chain: "C" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3696 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 13, 'TRANS': 468} Chain breaks: 1 Chain: "D" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4146 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 20, 'TRANS': 490} Chain: "E" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3696 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 13, 'TRANS': 468} Chain breaks: 1 Chain: "F" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4146 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 20, 'TRANS': 490} Time building chain proxies: 6.01, per 1000 atoms: 0.26 Number of scatterers: 23526 At special positions: 0 Unit cell: (115.056, 209.808, 172.96, 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 198 16.00 O 4491 8.00 N 3978 7.00 C 14859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=75, symmetry=0 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 401 " distance=2.03 Simple disulfide: pdb=" SG CYS A 447 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 460 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 494 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 554 " - pdb=" SG CYS A 605 " distance=2.04 Simple disulfide: pdb=" SG CYS A 569 " - pdb=" SG CYS A 635 " distance=2.04 Simple disulfide: pdb=" SG CYS A 583 " - pdb=" SG CYS A 593 " distance=2.03 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 663 " distance=2.03 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 688 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 702 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 48 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 55 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 221 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 286 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 392 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 401 " distance=2.03 Simple disulfide: pdb=" SG CYS C 447 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 458 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 460 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 494 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 510 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 547 " distance=2.03 Simple disulfide: pdb=" SG CYS C 554 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 569 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 583 " - pdb=" SG CYS C 593 " distance=2.03 Simple disulfide: pdb=" SG CYS C 600 " - pdb=" SG CYS C 663 " distance=2.03 Simple disulfide: pdb=" SG CYS C 657 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 694 " distance=2.03 Simple disulfide: pdb=" SG CYS C 688 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 702 " - pdb=" SG CYS C 711 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS D 177 " - pdb=" SG CYS D 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 221 " distance=2.03 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 286 " distance=2.03 Simple disulfide: pdb=" SG CYS E 349 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 392 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 394 " - pdb=" SG CYS E 401 " distance=2.03 Simple disulfide: pdb=" SG CYS E 447 " - pdb=" SG CYS E 477 " distance=2.03 Simple disulfide: pdb=" SG CYS E 458 " - pdb=" SG CYS E 474 " distance=2.03 Simple disulfide: pdb=" SG CYS E 460 " - pdb=" SG CYS E 466 " distance=2.03 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 494 " distance=2.03 Simple disulfide: pdb=" SG CYS E 485 " - pdb=" SG CYS E 491 " distance=2.03 Simple disulfide: pdb=" SG CYS E 490 " - pdb=" SG CYS E 516 " distance=2.03 Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 523 " distance=2.03 Simple disulfide: pdb=" SG CYS E 510 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 535 " - pdb=" SG CYS E 547 " distance=2.03 Simple disulfide: pdb=" SG CYS E 554 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 569 " - pdb=" SG CYS E 635 " distance=2.03 Simple disulfide: pdb=" SG CYS E 583 " - pdb=" SG CYS E 593 " distance=2.03 Simple disulfide: pdb=" SG CYS E 600 " - pdb=" SG CYS E 663 " distance=2.03 Simple disulfide: pdb=" SG CYS E 657 " - pdb=" SG CYS E 668 " distance=2.02 Simple disulfide: pdb=" SG CYS E 679 " - pdb=" SG CYS E 694 " distance=2.03 Simple disulfide: pdb=" SG CYS E 688 " - pdb=" SG CYS E 700 " distance=2.03 Simple disulfide: pdb=" SG CYS E 702 " - pdb=" SG CYS E 711 " distance=2.03 Simple disulfide: pdb=" SG CYS F 42 " - pdb=" SG CYS F 48 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 55 " distance=2.03 Simple disulfide: pdb=" SG CYS F 177 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 221 " distance=2.03 Simple disulfide: pdb=" SG CYS F 260 " - pdb=" SG CYS F 286 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 57 sheets defined 14.2% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 258 through 282 removed outlier: 3.960A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 319 Processing helix chain 'A' and resid 366 through 378 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 415 through 428 Processing helix chain 'A' and resid 431 through 435 removed outlier: 4.115A pdb=" N PHE A 435 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'A' and resid 549 through 558 removed outlier: 3.686A pdb=" N GLN A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 removed outlier: 4.045A pdb=" N TYR A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.620A pdb=" N THR B 134 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 135' Processing helix chain 'B' and resid 178 through 191 removed outlier: 4.475A pdb=" N TRP B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'C' and resid 248 through 255 removed outlier: 3.778A pdb=" N PHE C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 279 removed outlier: 3.981A pdb=" N ASP C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 319 Processing helix chain 'C' and resid 362 through 378 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.720A pdb=" N ILE C 419 " --> pdb=" O THR C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.717A pdb=" N LEU C 434 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE C 435 " --> pdb=" O ALA C 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 431 through 435' Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.868A pdb=" N VAL C 467 " --> pdb=" O PRO C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 558 Processing helix chain 'C' and resid 566 through 574 removed outlier: 3.733A pdb=" N TYR C 570 " --> pdb=" O ASP C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 removed outlier: 4.087A pdb=" N PHE C 674 " --> pdb=" O PRO C 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 181 through 189 removed outlier: 3.993A pdb=" N VAL D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'E' and resid 248 through 255 Processing helix chain 'E' and resid 258 through 278 Processing helix chain 'E' and resid 304 through 320 Processing helix chain 'E' and resid 362 through 378 Processing helix chain 'E' and resid 383 through 389 Processing helix chain 'E' and resid 415 through 429 removed outlier: 3.646A pdb=" N GLY E 429 " --> pdb=" O PHE E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 467 Processing helix chain 'E' and resid 549 through 558 Processing helix chain 'E' and resid 566 through 574 removed outlier: 3.628A pdb=" N TYR E 570 " --> pdb=" O ASP E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 675 Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 181 through 191 Processing helix chain 'F' and resid 215 through 219 Processing sheet with id=AA1, first strand: chain 'A' and resid 284 through 292 removed outlier: 5.848A pdb=" N ILE A 241 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 288 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 243 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N MET A 290 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 245 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N THR A 292 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN A 247 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ALA A 326 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU A 242 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N HIS A 328 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N MET A 244 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE A 330 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 246 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA3, first strand: chain 'A' and resid 502 through 504 removed outlier: 4.005A pdb=" N ARG A 504 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 511 through 512 removed outlier: 4.587A pdb=" N ILE A 527 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AA7, first strand: chain 'A' and resid 622 through 624 Processing sheet with id=AA8, first strand: chain 'A' and resid 661 through 663 Processing sheet with id=AA9, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 55 removed outlier: 5.714A pdb=" N SER B 73 " --> pdb=" O CYS B 55 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 97 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 96 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLU B 123 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE B 98 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AB3, first strand: chain 'B' and resid 199 through 201 Processing sheet with id=AB4, first strand: chain 'B' and resid 227 through 230 removed outlier: 5.775A pdb=" N LYS B 228 " --> pdb=" O LYS B 549 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS B 549 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 241 through 244 Processing sheet with id=AB6, first strand: chain 'B' and resid 253 through 254 removed outlier: 3.836A pdb=" N LYS B 259 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N CYS B 260 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN B 277 " --> pdb=" O CYS B 260 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE B 262 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 264 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 273 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 283 through 291 removed outlier: 5.197A pdb=" N LEU B 295 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 308 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 334 through 340 removed outlier: 3.936A pdb=" N ASP B 334 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 336 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 360 through 362 Processing sheet with id=AC1, first strand: chain 'B' and resid 381 through 383 Processing sheet with id=AC2, first strand: chain 'B' and resid 381 through 383 removed outlier: 3.786A pdb=" N TRP B 413 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 436 through 438 removed outlier: 3.593A pdb=" N LYS B 436 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS B 459 " --> pdb=" O ASP B 467 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP B 467 " --> pdb=" O LYS B 459 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 479 through 484 removed outlier: 5.629A pdb=" N GLN B 488 " --> pdb=" O TRP B 504 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA B 490 " --> pdb=" O TYR B 502 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 502 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 492 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THR B 499 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B 516 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 501 " --> pdb=" O PHE B 514 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 283 through 292 removed outlier: 6.533A pdb=" N LYS C 239 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE C 285 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE C 241 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU C 287 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU C 243 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 289 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA C 326 " --> pdb=" O TYR C 240 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU C 242 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N HIS C 328 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N MET C 244 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N PHE C 330 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 246 " --> pdb=" O PHE C 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 474 through 475 Processing sheet with id=AC7, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AC8, first strand: chain 'C' and resid 502 through 504 removed outlier: 3.673A pdb=" N ARG C 504 " --> pdb=" O GLU C 514 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 541 through 543 Processing sheet with id=AD1, first strand: chain 'C' and resid 563 through 564 removed outlier: 3.565A pdb=" N THR C 563 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 656 through 658 removed outlier: 6.309A pdb=" N MET C 661 " --> pdb=" O CYS C 657 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 693 through 694 removed outlier: 3.883A pdb=" N VAL C 693 " --> pdb=" O VAL C 701 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 46 through 48 removed outlier: 6.453A pdb=" N ALA D 53 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL D 75 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS D 55 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 196 " --> pdb=" O VAL D 168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 105 through 106 Processing sheet with id=AD6, first strand: chain 'D' and resid 226 through 228 removed outlier: 4.419A pdb=" N ASN D 534 " --> pdb=" O HIS D 550 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 239 through 242 removed outlier: 6.376A pdb=" N CYS D 260 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN D 277 " --> pdb=" O CYS D 260 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE D 262 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 283 through 287 removed outlier: 7.073A pdb=" N ALA D 300 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS D 286 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE D 298 " --> pdb=" O CYS D 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 283 through 287 removed outlier: 7.073A pdb=" N ALA D 300 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS D 286 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE D 298 " --> pdb=" O CYS D 286 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 295 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE D 308 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 332 through 340 removed outlier: 3.768A pdb=" N ASP D 334 " --> pdb=" O ALA D 349 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 381 through 387 removed outlier: 5.188A pdb=" N SER D 403 " --> pdb=" O ARG D 407 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 434 through 440 removed outlier: 3.526A pdb=" N LYS D 436 " --> pdb=" O CYS D 447 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL D 444 " --> pdb=" O TRP D 460 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER D 455 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA D 470 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL D 457 " --> pdb=" O ILE D 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 479 through 484 removed outlier: 6.089A pdb=" N GLN D 488 " --> pdb=" O TRP D 504 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR D 499 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU D 516 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL D 501 " --> pdb=" O PHE D 514 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 283 through 292 removed outlier: 7.580A pdb=" N ILE E 245 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N MET E 290 " --> pdb=" O ILE E 245 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASN E 247 " --> pdb=" O MET E 290 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR E 292 " --> pdb=" O ASN E 247 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 491 through 492 Processing sheet with id=AE7, first strand: chain 'E' and resid 502 through 504 removed outlier: 4.049A pdb=" N ARG E 504 " --> pdb=" O GLU E 514 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 541 through 543 Processing sheet with id=AE9, first strand: chain 'E' and resid 563 through 564 Processing sheet with id=AF1, first strand: chain 'E' and resid 622 through 624 Processing sheet with id=AF2, first strand: chain 'E' and resid 661 through 663 Processing sheet with id=AF3, first strand: chain 'E' and resid 693 through 694 removed outlier: 3.962A pdb=" N VAL E 693 " --> pdb=" O VAL E 701 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.009A pdb=" N LEU F 96 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU F 123 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE F 98 " --> pdb=" O GLU F 123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 199 through 201 removed outlier: 4.724A pdb=" N ARG F 209 " --> pdb=" O CYS F 200 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 225 through 232 removed outlier: 6.665A pdb=" N ILE F 547 " --> pdb=" O SER F 229 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP F 231 " --> pdb=" O THR F 545 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR F 545 " --> pdb=" O ASP F 231 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN F 534 " --> pdb=" O HIS F 550 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 239 through 244 removed outlier: 7.551A pdb=" N GLU F 248 " --> pdb=" O TRP F 265 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP F 265 " --> pdb=" O GLU F 248 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS F 260 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN F 277 " --> pdb=" O CYS F 260 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE F 262 " --> pdb=" O TYR F 275 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 283 through 291 removed outlier: 6.068A pdb=" N LEU F 295 " --> pdb=" O ARG F 311 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 308 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 332 through 340 removed outlier: 4.283A pdb=" N ASP F 334 " --> pdb=" O ALA F 349 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA F 349 " --> pdb=" O ASP F 334 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP F 344 " --> pdb=" O TRP F 362 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR F 357 " --> pdb=" O SER F 372 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER F 372 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE F 359 " --> pdb=" O HIS F 370 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR F 368 " --> pdb=" O LYS F 361 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 379 through 387 removed outlier: 4.986A pdb=" N SER F 403 " --> pdb=" O ARG F 407 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG F 407 " --> pdb=" O SER F 403 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 437 through 440 removed outlier: 5.446A pdb=" N VAL F 444 " --> pdb=" O TRP F 460 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LYS F 459 " --> pdb=" O ASP F 467 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP F 467 " --> pdb=" O LYS F 459 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 480 through 484 removed outlier: 6.669A pdb=" N GLN F 488 " --> pdb=" O TRP F 504 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN F 500 " --> pdb=" O LEU F 492 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR F 499 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU F 516 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL F 501 " --> pdb=" O PHE F 514 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN F 503 " --> pdb=" O VAL F 512 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL F 512 " --> pdb=" O ASN F 503 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 2.60 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: 7661 1.34 - 1.46: 5598 1.46 - 1.58: 10534 1.58 - 1.70: 0 1.70 - 1.82: 243 Bond restraints: 24036 Sorted by residual: bond pdb=" C GLN B 406 " pdb=" N ARG B 407 " ideal model delta sigma weight residual 1.339 1.230 0.109 5.57e-02 3.22e+02 3.86e+00 bond pdb=" CA CYS B 447 " pdb=" CB CYS B 447 " ideal model delta sigma weight residual 1.528 1.491 0.038 2.61e-02 1.47e+03 2.08e+00 bond pdb=" CB VAL B 382 " pdb=" CG1 VAL B 382 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CG1 ILE B 335 " pdb=" CD1 ILE B 335 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.37e+00 bond pdb=" C ALA B 470 " pdb=" N MET B 471 " ideal model delta sigma weight residual 1.333 1.364 -0.032 2.74e-02 1.33e+03 1.32e+00 ... (remaining 24031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 31859 1.72 - 3.44: 550 3.44 - 5.17: 59 5.17 - 6.89: 16 6.89 - 8.61: 3 Bond angle restraints: 32487 Sorted by residual: angle pdb=" N ILE D 70 " pdb=" CA ILE D 70 " pdb=" C ILE D 70 " ideal model delta sigma weight residual 112.96 108.84 4.12 1.00e+00 1.00e+00 1.70e+01 angle pdb=" C ASP B 467 " pdb=" N ILE B 468 " pdb=" CA ILE B 468 " ideal model delta sigma weight residual 123.16 119.34 3.82 1.06e+00 8.90e-01 1.30e+01 angle pdb=" CB MET A 403 " pdb=" CG MET A 403 " pdb=" SD MET A 403 " ideal model delta sigma weight residual 112.70 121.31 -8.61 3.00e+00 1.11e-01 8.24e+00 angle pdb=" CA MET C 290 " pdb=" CB MET C 290 " pdb=" CG MET C 290 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.94e+00 angle pdb=" C THR B 380 " pdb=" N ASP B 381 " pdb=" CA ASP B 381 " ideal model delta sigma weight residual 121.63 116.65 4.98 1.92e+00 2.71e-01 6.71e+00 ... (remaining 32482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 12997 18.05 - 36.09: 1293 36.09 - 54.14: 246 54.14 - 72.18: 31 72.18 - 90.23: 13 Dihedral angle restraints: 14580 sinusoidal: 5955 harmonic: 8625 Sorted by residual: dihedral pdb=" CB CYS D 260 " pdb=" SG CYS D 260 " pdb=" SG CYS D 286 " pdb=" CB CYS D 286 " ideal model delta sinusoidal sigma weight residual 93.00 -176.77 -90.23 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS E 569 " pdb=" SG CYS E 569 " pdb=" SG CYS E 635 " pdb=" CB CYS E 635 " ideal model delta sinusoidal sigma weight residual 93.00 -178.87 -88.13 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS B 260 " pdb=" SG CYS B 260 " pdb=" SG CYS B 286 " pdb=" CB CYS B 286 " ideal model delta sinusoidal sigma weight residual 93.00 178.39 -85.39 1 1.00e+01 1.00e-02 8.83e+01 ... (remaining 14577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2544 0.041 - 0.082: 705 0.082 - 0.123: 274 0.123 - 0.164: 35 0.164 - 0.204: 3 Chirality restraints: 3561 Sorted by residual: chirality pdb=" CG LEU F 170 " pdb=" CB LEU F 170 " pdb=" CD1 LEU F 170 " pdb=" CD2 LEU F 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB THR B 224 " pdb=" CA THR B 224 " pdb=" OG1 THR B 224 " pdb=" CG2 THR B 224 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CB ILE A 241 " pdb=" CA ILE A 241 " pdb=" CG1 ILE A 241 " pdb=" CG2 ILE A 241 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 3558 not shown) Planarity restraints: 4185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 293 " 0.014 2.00e-02 2.50e+03 1.27e-02 4.06e+00 pdb=" CG TRP C 293 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP C 293 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 293 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 293 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 293 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 293 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 293 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 293 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 293 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET F 471 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO F 472 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 472 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 472 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 423 " 0.013 2.00e-02 2.50e+03 1.24e-02 2.30e+00 pdb=" CG HIS C 423 " -0.014 2.00e-02 2.50e+03 pdb=" ND1 HIS C 423 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS C 423 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS C 423 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 HIS C 423 " -0.002 2.00e-02 2.50e+03 ... (remaining 4182 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 451 2.63 - 3.20: 22280 3.20 - 3.77: 38600 3.77 - 4.33: 53095 4.33 - 4.90: 84316 Nonbonded interactions: 198742 Sorted by model distance: nonbonded pdb=" OD1 ASN A 358 " pdb=" OG SER A 373 " model vdw 2.065 3.040 nonbonded pdb=" O LYS F 139 " pdb=" OG SER F 164 " model vdw 2.138 3.040 nonbonded pdb=" OG1 THR B 47 " pdb=" O LEU B 54 " model vdw 2.146 3.040 nonbonded pdb=" OG SER A 337 " pdb=" O ARG A 339 " model vdw 2.154 3.040 nonbonded pdb=" OH TYR A 344 " pdb=" OE2 GLU A 644 " model vdw 2.171 3.040 ... (remaining 198737 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.640 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4154 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 : 0.003 0.109 24111 Z= 0.150 Angle : 0.572 8.612 32637 Z= 0.308 Chirality : 0.044 0.204 3561 Planarity : 0.003 0.040 4185 Dihedral : 13.958 85.548 8811 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 aren not related in a simple way. whole: -1.72 (0.15), residues: 2961 helix: 0.58 (0.28), residues: 352 sheet: -1.38 (0.20), residues: 675 loop : -1.42 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 209 TYR 0.014 0.001 TYR A 408 PHE 0.019 0.002 PHE B 451 TRP 0.033 0.001 TRP C 293 HIS 0.012 0.001 HIS D 398 Details of bonding type rmsd covalent geometry : bond 0.00342 (24036) covalent geometry : angle 0.56933 (32487) SS BOND : bond 0.00214 ( 75) SS BOND : angle 1.02654 ( 150) hydrogen bonds : bond 0.19167 ( 632) hydrogen bonds : angle 8.48342 ( 1668) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 LEU cc_start: 0.7532 (mm) cc_final: 0.6702 (tt) REVERT: C 403 MET cc_start: 0.1927 (mpp) cc_final: -0.0472 (mmt) REVERT: C 530 MET cc_start: 0.4615 (tmm) cc_final: 0.3902 (tmm) REVERT: C 661 MET cc_start: 0.4803 (tpp) cc_final: 0.4524 (tpt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1646 time to fit residues: 59.8314 Evaluate side-chains 147 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 40.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 50.0000 overall best weight: 3.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS B 322 GLN B 406 GLN ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN C 497 GLN D 149 ASN D 374 HIS ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** E 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 HIS ** F 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.193182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5007 r_free = 0.5007 target = 0.185745 restraints weight = 71648.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.184242 restraints weight = 52793.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.181860 restraints weight = 71076.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.181537 restraints weight = 76209.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.180666 restraints weight = 69513.312| |-----------------------------------------------------------------------------| r_work (final): 0.4940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4640 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 24111 Z= 0.189 Angle : 0.617 8.890 32637 Z= 0.327 Chirality : 0.045 0.209 3561 Planarity : 0.004 0.044 4185 Dihedral : 4.628 20.458 3186 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.75 % Allowed : 7.92 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.15), residues: 2961 helix: 0.70 (0.27), residues: 365 sheet: -1.39 (0.19), residues: 677 loop : -1.50 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 504 TYR 0.024 0.002 TYR A 240 PHE 0.019 0.002 PHE F 451 TRP 0.016 0.002 TRP B 265 HIS 0.008 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00438 (24036) covalent geometry : angle 0.61460 (32487) SS BOND : bond 0.00237 ( 75) SS BOND : angle 1.02035 ( 150) hydrogen bonds : bond 0.04542 ( 632) hydrogen bonds : angle 6.96586 ( 1668) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 374 LEU cc_start: 0.7635 (mm) cc_final: 0.6803 (tt) REVERT: A 530 MET cc_start: 0.6144 (tpp) cc_final: 0.5861 (tpp) REVERT: C 403 MET cc_start: 0.2079 (mpp) cc_final: -0.0356 (mmt) REVERT: C 530 MET cc_start: 0.4493 (tmm) cc_final: 0.2927 (tmm) REVERT: D 169 ASP cc_start: 0.3892 (m-30) cc_final: 0.3417 (m-30) REVERT: E 616 GLU cc_start: -0.0036 (tm-30) cc_final: -0.1432 (mm-30) outliers start: 20 outliers final: 14 residues processed: 176 average time/residue: 0.1446 time to fit residues: 43.5123 Evaluate side-chains 160 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 437 HIS Chi-restraints excluded: chain F residue 536 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 65 optimal weight: 20.0000 chunk 116 optimal weight: 40.0000 chunk 234 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 27 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 ASN ** E 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 553 GLN F 437 HIS ** F 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.192407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.183449 restraints weight = 71720.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.181296 restraints weight = 63244.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.180406 restraints weight = 79640.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.180160 restraints weight = 64707.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.179723 restraints weight = 66415.232| |-----------------------------------------------------------------------------| r_work (final): 0.4928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4693 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 24111 Z= 0.207 Angle : 0.623 8.181 32637 Z= 0.329 Chirality : 0.044 0.161 3561 Planarity : 0.004 0.068 4185 Dihedral : 4.678 21.482 3186 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.47 % Allowed : 11.61 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.15), residues: 2961 helix: 0.65 (0.27), residues: 365 sheet: -1.48 (0.19), residues: 683 loop : -1.54 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 132 TYR 0.021 0.002 TYR B 119 PHE 0.021 0.002 PHE B 226 TRP 0.016 0.002 TRP B 460 HIS 0.010 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00483 (24036) covalent geometry : angle 0.62000 (32487) SS BOND : bond 0.00235 ( 75) SS BOND : angle 1.02931 ( 150) hydrogen bonds : bond 0.04018 ( 632) hydrogen bonds : angle 6.77575 ( 1668) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5511 (mtp) REVERT: A 374 LEU cc_start: 0.7675 (mm) cc_final: 0.6755 (tt) REVERT: B 267 HIS cc_start: 0.5970 (OUTLIER) cc_final: 0.5616 (t-90) REVERT: C 313 MET cc_start: 0.7225 (mmm) cc_final: 0.6991 (mmt) REVERT: C 403 MET cc_start: 0.2041 (mpp) cc_final: -0.0410 (mmt) REVERT: E 244 MET cc_start: 0.3694 (tpt) cc_final: 0.2769 (tpt) REVERT: E 290 MET cc_start: 0.2499 (mmm) cc_final: 0.2124 (mmm) REVERT: E 313 MET cc_start: 0.3828 (mmm) cc_final: 0.3621 (mmp) REVERT: E 616 GLU cc_start: -0.0155 (tm-30) cc_final: -0.1459 (mm-30) outliers start: 39 outliers final: 23 residues processed: 183 average time/residue: 0.1331 time to fit residues: 42.1291 Evaluate side-chains 169 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 536 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 30.0000 chunk 70 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 276 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 182 optimal weight: 40.0000 chunk 51 optimal weight: 30.0000 chunk 163 optimal weight: 0.0040 chunk 198 optimal weight: 50.0000 chunk 295 optimal weight: 20.0000 chunk 135 optimal weight: 0.0010 overall best weight: 0.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS B 149 ASN B 406 GLN C 497 GLN D 152 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5130 r_free = 0.5130 target = 0.194642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.186106 restraints weight = 72115.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.184587 restraints weight = 77923.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.183160 restraints weight = 73214.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.182918 restraints weight = 75754.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.182390 restraints weight = 68309.649| |-----------------------------------------------------------------------------| r_work (final): 0.4961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4564 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24111 Z= 0.104 Angle : 0.549 9.961 32637 Z= 0.286 Chirality : 0.043 0.166 3561 Planarity : 0.003 0.041 4185 Dihedral : 4.355 21.421 3186 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.47 % Allowed : 13.35 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.15), residues: 2961 helix: 0.84 (0.27), residues: 366 sheet: -1.26 (0.20), residues: 644 loop : -1.51 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 378 TYR 0.022 0.001 TYR B 119 PHE 0.021 0.001 PHE B 159 TRP 0.020 0.001 TRP B 265 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.00229 (24036) covalent geometry : angle 0.54728 (32487) SS BOND : bond 0.00191 ( 75) SS BOND : angle 0.80101 ( 150) hydrogen bonds : bond 0.03228 ( 632) hydrogen bonds : angle 6.25242 ( 1668) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.5802 (OUTLIER) cc_final: 0.5459 (ttt) REVERT: A 374 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6555 (tt) REVERT: B 267 HIS cc_start: 0.5787 (OUTLIER) cc_final: 0.5509 (t-90) REVERT: C 313 MET cc_start: 0.7119 (mmm) cc_final: 0.6843 (mmt) REVERT: C 403 MET cc_start: 0.2162 (mpp) cc_final: -0.0352 (mmt) REVERT: E 244 MET cc_start: 0.3391 (tpt) cc_final: 0.2222 (tpt) REVERT: E 616 GLU cc_start: -0.0226 (tm-30) cc_final: -0.1334 (mm-30) outliers start: 39 outliers final: 17 residues processed: 191 average time/residue: 0.1389 time to fit residues: 45.7819 Evaluate side-chains 169 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 536 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 50 optimal weight: 6.9990 chunk 139 optimal weight: 40.0000 chunk 292 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 101 optimal weight: 40.0000 chunk 283 optimal weight: 6.9990 chunk 206 optimal weight: 50.0000 chunk 95 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 232 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS B 406 GLN ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 HIS C 717 HIS D 152 GLN ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.190625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.182767 restraints weight = 71011.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.180398 restraints weight = 57901.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.179575 restraints weight = 69137.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.178829 restraints weight = 72846.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.178142 restraints weight = 80702.979| |-----------------------------------------------------------------------------| r_work (final): 0.4906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4758 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.222 24111 Z= 0.299 Angle : 0.723 10.491 32637 Z= 0.379 Chirality : 0.046 0.225 3561 Planarity : 0.004 0.051 4185 Dihedral : 4.908 21.458 3186 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.70 % Favored : 92.27 % Rotamer: Outliers : 2.53 % Allowed : 14.82 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.15), residues: 2961 helix: 0.62 (0.27), residues: 359 sheet: -1.69 (0.19), residues: 673 loop : -1.63 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 171 TYR 0.026 0.002 TYR B 296 PHE 0.034 0.002 PHE B 226 TRP 0.021 0.002 TRP B 460 HIS 0.013 0.002 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00703 (24036) covalent geometry : angle 0.72152 (32487) SS BOND : bond 0.00316 ( 75) SS BOND : angle 0.92616 ( 150) hydrogen bonds : bond 0.04295 ( 632) hydrogen bonds : angle 6.72366 ( 1668) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 145 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.5993 (OUTLIER) cc_final: 0.5554 (mtp) REVERT: A 336 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: A 530 MET cc_start: 0.6334 (tpp) cc_final: 0.5995 (tpp) REVERT: A 608 ILE cc_start: 0.1906 (OUTLIER) cc_final: 0.1623 (mt) REVERT: B 267 HIS cc_start: 0.5951 (OUTLIER) cc_final: 0.5470 (t-90) REVERT: B 530 ILE cc_start: 0.4564 (OUTLIER) cc_final: 0.4291 (mt) REVERT: C 313 MET cc_start: 0.7220 (mmm) cc_final: 0.6945 (mmt) REVERT: C 403 MET cc_start: 0.2278 (mpp) cc_final: -0.0296 (mmt) REVERT: E 244 MET cc_start: 0.3508 (tpt) cc_final: 0.2212 (tpt) REVERT: E 290 MET cc_start: 0.2820 (mmm) cc_final: 0.1979 (mmm) REVERT: F 114 LEU cc_start: 0.5344 (OUTLIER) cc_final: 0.4981 (pp) outliers start: 67 outliers final: 42 residues processed: 201 average time/residue: 0.1356 time to fit residues: 47.2300 Evaluate side-chains 180 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 437 HIS Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 536 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 45 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 190 optimal weight: 8.9990 chunk 296 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 50.0000 chunk 114 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 163 optimal weight: 7.9990 chunk 118 optimal weight: 50.0000 chunk 79 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN C 639 HIS D 152 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.193997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.185348 restraints weight = 72536.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.183845 restraints weight = 81697.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.182960 restraints weight = 74724.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.182777 restraints weight = 73982.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.181997 restraints weight = 70816.072| |-----------------------------------------------------------------------------| r_work (final): 0.4958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4572 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24111 Z= 0.108 Angle : 0.575 10.735 32637 Z= 0.298 Chirality : 0.044 0.169 3561 Planarity : 0.004 0.063 4185 Dihedral : 4.491 27.340 3186 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.73 % Allowed : 16.29 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.15), residues: 2961 helix: 0.84 (0.27), residues: 360 sheet: -1.50 (0.19), residues: 674 loop : -1.53 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.018 0.001 TYR B 119 PHE 0.017 0.001 PHE F 346 TRP 0.022 0.001 TRP B 265 HIS 0.008 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00244 (24036) covalent geometry : angle 0.57210 (32487) SS BOND : bond 0.00174 ( 75) SS BOND : angle 1.04951 ( 150) hydrogen bonds : bond 0.03179 ( 632) hydrogen bonds : angle 6.17370 ( 1668) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5424 (ttt) REVERT: A 530 MET cc_start: 0.6122 (tpp) cc_final: 0.5738 (tpp) REVERT: A 608 ILE cc_start: 0.1908 (OUTLIER) cc_final: 0.1663 (mt) REVERT: B 267 HIS cc_start: 0.5713 (OUTLIER) cc_final: 0.5121 (t-90) REVERT: C 403 MET cc_start: 0.2324 (mpp) cc_final: -0.0242 (mmt) REVERT: E 244 MET cc_start: 0.3194 (tpt) cc_final: 0.2179 (tpt) REVERT: E 290 MET cc_start: 0.2637 (mmm) cc_final: 0.1749 (mmm) REVERT: E 616 GLU cc_start: -0.0614 (tm-30) cc_final: -0.1335 (mm-30) outliers start: 46 outliers final: 29 residues processed: 195 average time/residue: 0.1369 time to fit residues: 46.0491 Evaluate side-chains 175 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 437 HIS Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 536 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 224 optimal weight: 8.9990 chunk 242 optimal weight: 0.9990 chunk 146 optimal weight: 40.0000 chunk 226 optimal weight: 20.0000 chunk 220 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 99 optimal weight: 60.0000 chunk 133 optimal weight: 50.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS B 406 GLN ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 HIS D 152 GLN ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5100 r_free = 0.5100 target = 0.191928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.183252 restraints weight = 71128.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.181015 restraints weight = 59542.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.180039 restraints weight = 67593.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.179481 restraints weight = 63303.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.179061 restraints weight = 61685.656| |-----------------------------------------------------------------------------| r_work (final): 0.4921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4716 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 24111 Z= 0.198 Angle : 0.622 11.121 32637 Z= 0.324 Chirality : 0.044 0.179 3561 Planarity : 0.004 0.044 4185 Dihedral : 4.618 21.901 3186 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.30 % Allowed : 16.97 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.15), residues: 2961 helix: 0.85 (0.27), residues: 358 sheet: -1.58 (0.19), residues: 679 loop : -1.57 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 450 TYR 0.021 0.002 TYR B 119 PHE 0.023 0.002 PHE B 226 TRP 0.024 0.001 TRP B 265 HIS 0.009 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00469 (24036) covalent geometry : angle 0.62079 (32487) SS BOND : bond 0.00222 ( 75) SS BOND : angle 0.89681 ( 150) hydrogen bonds : bond 0.03539 ( 632) hydrogen bonds : angle 6.26418 ( 1668) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 147 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.5799 (OUTLIER) cc_final: 0.5370 (mtp) REVERT: A 530 MET cc_start: 0.6148 (tpp) cc_final: 0.5815 (tpp) REVERT: A 608 ILE cc_start: 0.1973 (OUTLIER) cc_final: 0.1709 (mt) REVERT: B 267 HIS cc_start: 0.5484 (OUTLIER) cc_final: 0.5009 (t-90) REVERT: C 403 MET cc_start: 0.2311 (mpp) cc_final: -0.0207 (mmt) REVERT: E 244 MET cc_start: 0.3329 (tpt) cc_final: 0.2081 (tpt) REVERT: E 290 MET cc_start: 0.2764 (mmm) cc_final: 0.1853 (mmm) REVERT: E 616 GLU cc_start: -0.0514 (tm-30) cc_final: -0.1708 (mm-30) outliers start: 61 outliers final: 47 residues processed: 195 average time/residue: 0.1393 time to fit residues: 46.9749 Evaluate side-chains 191 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain C residue 401 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain E residue 531 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 437 HIS Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 536 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 29 optimal weight: 50.0000 chunk 70 optimal weight: 0.9990 chunk 115 optimal weight: 0.0570 chunk 219 optimal weight: 0.0980 chunk 40 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 188 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS B 406 GLN ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN D 342 ASN ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5123 r_free = 0.5123 target = 0.193735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5022 r_free = 0.5022 target = 0.186501 restraints weight = 71589.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.183343 restraints weight = 46913.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.181764 restraints weight = 63368.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.181361 restraints weight = 60924.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.180917 restraints weight = 58832.164| |-----------------------------------------------------------------------------| r_work (final): 0.4947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4627 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 24111 Z= 0.111 Angle : 0.567 12.302 32637 Z= 0.292 Chirality : 0.043 0.165 3561 Planarity : 0.003 0.039 4185 Dihedral : 4.395 20.809 3186 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.89 % Allowed : 17.38 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.15), residues: 2961 helix: 0.99 (0.27), residues: 360 sheet: -1.34 (0.20), residues: 665 loop : -1.52 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 132 TYR 0.018 0.001 TYR B 119 PHE 0.017 0.001 PHE F 346 TRP 0.031 0.001 TRP B 265 HIS 0.008 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00250 (24036) covalent geometry : angle 0.56570 (32487) SS BOND : bond 0.00174 ( 75) SS BOND : angle 0.79410 ( 150) hydrogen bonds : bond 0.03053 ( 632) hydrogen bonds : angle 6.00425 ( 1668) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.5724 (OUTLIER) cc_final: 0.5292 (ttt) REVERT: A 530 MET cc_start: 0.6113 (tpp) cc_final: 0.5791 (tpp) REVERT: A 608 ILE cc_start: 0.1921 (OUTLIER) cc_final: 0.1659 (mt) REVERT: B 267 HIS cc_start: 0.5327 (OUTLIER) cc_final: 0.4895 (t-90) REVERT: C 403 MET cc_start: 0.2360 (mpp) cc_final: -0.0270 (mmt) REVERT: E 244 MET cc_start: 0.3108 (tpt) cc_final: 0.1952 (tpt) REVERT: E 616 GLU cc_start: -0.0685 (tm-30) cc_final: -0.1702 (mm-30) REVERT: F 336 GLU cc_start: 0.6533 (tm-30) cc_final: 0.6263 (tm-30) outliers start: 50 outliers final: 37 residues processed: 197 average time/residue: 0.1390 time to fit residues: 46.8437 Evaluate side-chains 182 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain C residue 401 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 437 HIS Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 536 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 26 optimal weight: 50.0000 chunk 277 optimal weight: 9.9990 chunk 209 optimal weight: 30.0000 chunk 95 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 235 optimal weight: 0.4980 chunk 208 optimal weight: 0.7980 chunk 278 optimal weight: 5.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS B 406 GLN ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.192944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.185535 restraints weight = 71872.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.182583 restraints weight = 49309.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.181064 restraints weight = 64664.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.180558 restraints weight = 61674.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.180318 restraints weight = 56165.021| |-----------------------------------------------------------------------------| r_work (final): 0.4940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4651 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 24111 Z= 0.148 Angle : 0.597 12.467 32637 Z= 0.307 Chirality : 0.044 0.269 3561 Planarity : 0.003 0.038 4185 Dihedral : 4.425 21.055 3186 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.96 % Allowed : 17.91 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.15), residues: 2961 helix: 0.94 (0.27), residues: 360 sheet: -1.38 (0.20), residues: 667 loop : -1.55 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 171 TYR 0.030 0.001 TYR B 548 PHE 0.024 0.002 PHE F 525 TRP 0.015 0.001 TRP B 265 HIS 0.010 0.001 HIS E 423 Details of bonding type rmsd covalent geometry : bond 0.00345 (24036) covalent geometry : angle 0.59551 (32487) SS BOND : bond 0.00195 ( 75) SS BOND : angle 0.81787 ( 150) hydrogen bonds : bond 0.03229 ( 632) hydrogen bonds : angle 5.96244 ( 1668) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5355 (mtp) REVERT: A 374 LEU cc_start: 0.7542 (mm) cc_final: 0.6685 (tt) REVERT: A 530 MET cc_start: 0.6212 (tpp) cc_final: 0.5917 (tpp) REVERT: A 608 ILE cc_start: 0.1921 (OUTLIER) cc_final: 0.1421 (mt) REVERT: B 267 HIS cc_start: 0.5381 (OUTLIER) cc_final: 0.4945 (t-90) REVERT: C 403 MET cc_start: 0.2329 (mpp) cc_final: -0.0167 (mmt) REVERT: E 244 MET cc_start: 0.3084 (tpt) cc_final: 0.1973 (tpt) REVERT: E 616 GLU cc_start: -0.0697 (tm-30) cc_final: -0.1719 (mm-30) REVERT: F 336 GLU cc_start: 0.6560 (tm-30) cc_final: 0.6292 (tm-30) outliers start: 52 outliers final: 42 residues processed: 183 average time/residue: 0.1269 time to fit residues: 41.0505 Evaluate side-chains 181 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain C residue 401 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 437 HIS Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 536 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 184 optimal weight: 6.9990 chunk 132 optimal weight: 50.0000 chunk 278 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 236 optimal weight: 8.9990 chunk 212 optimal weight: 40.0000 chunk 146 optimal weight: 0.0570 chunk 78 optimal weight: 0.5980 chunk 215 optimal weight: 10.0000 chunk 201 optimal weight: 30.0000 overall best weight: 2.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.192785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.185394 restraints weight = 71526.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.182850 restraints weight = 48973.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.181284 restraints weight = 63146.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.180610 restraints weight = 65130.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.180240 restraints weight = 58059.269| |-----------------------------------------------------------------------------| r_work (final): 0.4939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4649 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 24111 Z= 0.151 Angle : 0.604 13.541 32637 Z= 0.310 Chirality : 0.044 0.169 3561 Planarity : 0.004 0.040 4185 Dihedral : 4.445 21.514 3186 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.81 % Allowed : 18.06 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.15), residues: 2961 helix: 0.91 (0.27), residues: 366 sheet: -1.36 (0.20), residues: 670 loop : -1.55 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 171 TYR 0.021 0.001 TYR B 119 PHE 0.030 0.002 PHE F 525 TRP 0.015 0.001 TRP B 265 HIS 0.010 0.001 HIS E 423 Details of bonding type rmsd covalent geometry : bond 0.00354 (24036) covalent geometry : angle 0.60278 (32487) SS BOND : bond 0.00190 ( 75) SS BOND : angle 0.79510 ( 150) hydrogen bonds : bond 0.03224 ( 632) hydrogen bonds : angle 5.94859 ( 1668) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5364 (mtp) REVERT: A 374 LEU cc_start: 0.7541 (mm) cc_final: 0.6698 (tt) REVERT: A 530 MET cc_start: 0.6181 (tpp) cc_final: 0.5894 (tpp) REVERT: A 608 ILE cc_start: 0.1863 (OUTLIER) cc_final: 0.1402 (mt) REVERT: B 267 HIS cc_start: 0.5372 (OUTLIER) cc_final: 0.4922 (t-90) REVERT: C 403 MET cc_start: 0.2313 (mpp) cc_final: -0.0179 (mmt) REVERT: E 244 MET cc_start: 0.3056 (tpt) cc_final: 0.1861 (tpt) REVERT: E 290 MET cc_start: 0.2674 (mmm) cc_final: 0.1425 (mmt) REVERT: F 336 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6263 (tm-30) outliers start: 48 outliers final: 42 residues processed: 179 average time/residue: 0.1255 time to fit residues: 39.3764 Evaluate side-chains 178 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain C residue 401 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 437 HIS Chi-restraints excluded: chain F residue 458 MET Chi-restraints excluded: chain F residue 536 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 217 optimal weight: 30.0000 chunk 80 optimal weight: 0.9990 chunk 246 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 221 optimal weight: 30.0000 chunk 8 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 242 optimal weight: 50.0000 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5100 r_free = 0.5100 target = 0.191891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.183217 restraints weight = 71275.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.180960 restraints weight = 59749.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.179708 restraints weight = 70276.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.179155 restraints weight = 63461.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.178758 restraints weight = 64391.005| |-----------------------------------------------------------------------------| r_work (final): 0.4919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4725 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 24111 Z= 0.193 Angle : 0.633 13.099 32637 Z= 0.327 Chirality : 0.044 0.182 3561 Planarity : 0.004 0.041 4185 Dihedral : 4.581 23.264 3186 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.92 % Allowed : 18.40 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.15), residues: 2961 helix: 0.87 (0.27), residues: 366 sheet: -1.47 (0.20), residues: 676 loop : -1.56 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 171 TYR 0.023 0.002 TYR B 119 PHE 0.025 0.002 PHE F 525 TRP 0.016 0.001 TRP B 265 HIS 0.010 0.001 HIS E 423 Details of bonding type rmsd covalent geometry : bond 0.00455 (24036) covalent geometry : angle 0.63181 (32487) SS BOND : bond 0.00210 ( 75) SS BOND : angle 0.79189 ( 150) hydrogen bonds : bond 0.03430 ( 632) hydrogen bonds : angle 6.06908 ( 1668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3388.82 seconds wall clock time: 60 minutes 17.34 seconds (3617.34 seconds total)