Starting phenix.real_space_refine on Fri Mar 6 00:36:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q3e_13790/03_2026/7q3e_13790_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q3e_13790/03_2026/7q3e_13790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q3e_13790/03_2026/7q3e_13790_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q3e_13790/03_2026/7q3e_13790_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q3e_13790/03_2026/7q3e_13790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q3e_13790/03_2026/7q3e_13790.map" } resolution = 3.35 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= -0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 72 5.16 5 C 8511 2.51 5 N 2248 2.21 5 O 2420 1.98 5 H 13368 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26622 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 8899 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 529} Chain breaks: 4 Chain: "B" Number of atoms: 7967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 7967 Classifications: {'peptide': 503} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 480} Chain breaks: 6 Chain: "C" Number of atoms: 6161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6161 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 358} Chain breaks: 1 Chain: "D" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3563 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 12, 'TRANS': 213} Chain breaks: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.58, per 1000 atoms: 0.17 Number of scatterers: 26622 At special positions: 0 Unit cell: (89.44, 142.76, 135.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 3 15.00 O 2420 8.00 N 2248 7.00 C 8511 6.00 H 13368 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 840.7 milliseconds 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3146 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 12 sheets defined 40.1% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.945A pdb=" N LEU A 17 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 68 through 83 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.273A pdb=" N GLY A 126 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 456 through 467 Processing helix chain 'A' and resid 469 through 480 Processing helix chain 'A' and resid 485 through 502 removed outlier: 3.602A pdb=" N ARG A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 522 removed outlier: 4.403A pdb=" N PHE A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 531 through 552 removed outlier: 5.195A pdb=" N GLU A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Proline residue: A 538 - end of helix Processing helix chain 'A' and resid 556 through 567 removed outlier: 3.781A pdb=" N VAL A 564 " --> pdb=" O PHE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.735A pdb=" N TYR A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 582 Processing helix chain 'A' and resid 589 through 598 Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.822A pdb=" N ASP B 57 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.865A pdb=" N LYS B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 363 removed outlier: 3.720A pdb=" N GLU B 359 " --> pdb=" O CYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 420 Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.744A pdb=" N ALA B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 removed outlier: 4.081A pdb=" N HIS B 437 " --> pdb=" O PRO B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 removed outlier: 4.202A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 500 removed outlier: 3.683A pdb=" N ASP B 496 " --> pdb=" O THR B 492 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 535 through 549 Processing helix chain 'B' and resid 550 through 556 Processing helix chain 'B' and resid 625 through 638 Processing helix chain 'B' and resid 639 through 641 No H-bonds generated for 'chain 'B' and resid 639 through 641' Processing helix chain 'B' and resid 642 through 652 Processing helix chain 'B' and resid 661 through 666 removed outlier: 3.647A pdb=" N LEU B 665 " --> pdb=" O ALA B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 789 Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 825 through 860 removed outlier: 3.815A pdb=" N GLN B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 844 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE B 845 " --> pdb=" O SER B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 938 Processing helix chain 'C' and resid 39 through 55 removed outlier: 4.001A pdb=" N HIS C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 111 Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 120 through 128 removed outlier: 3.666A pdb=" N LEU C 124 " --> pdb=" O ASN C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 161 through 175 Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.858A pdb=" N LEU C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.651A pdb=" N LEU C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Proline residue: C 280 - end of helix Processing helix chain 'C' and resid 322 through 338 Processing helix chain 'C' and resid 396 through 398 No H-bonds generated for 'chain 'C' and resid 396 through 398' Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'D' and resid 14 through 17 Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 67 through 77 Processing helix chain 'D' and resid 118 through 125 removed outlier: 3.818A pdb=" N LYS D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 186 through 198 Processing helix chain 'D' and resid 221 through 245 removed outlier: 4.702A pdb=" N HIS D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 9.128A pdb=" N TYR A 27 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 8 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 372 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE A 382 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N LEU A 370 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 354 removed outlier: 3.915A pdb=" N LEU A 351 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N LEU A 370 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE A 382 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 372 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 92 removed outlier: 6.701A pdb=" N LEU A 99 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER A 88 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN A 97 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TRP A 90 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 95 " --> pdb=" O TRP A 90 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 105 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE A 120 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 107 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 118 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER A 109 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 200 removed outlier: 6.911A pdb=" N MET A 233 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE A 248 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU A 235 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 255 through 260 removed outlier: 6.796A pdb=" N VAL A 271 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL A 258 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE A 260 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN A 267 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A 283 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG A 302 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER A 285 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 300 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 287 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 309 through 314 removed outlier: 4.109A pdb=" N SER A 329 " --> pdb=" O CYS A 325 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 70 removed outlier: 4.238A pdb=" N TYR B 593 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 604 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 523 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS B 606 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER B 521 " --> pdb=" O CYS B 606 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU B 608 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER B 521 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER B 532 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 523 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 331 through 335 removed outlier: 6.020A pdb=" N ILE B 331 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 317 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR B 367 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG C 64 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER B 369 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER C 62 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 371 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU C 60 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N GLN C 59 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N ASN C 74 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN C 61 " --> pdb=" O TRP C 72 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA C 16 " --> pdb=" O PRO C 22 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 27 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478 removed outlier: 6.349A pdb=" N VAL B 477 " --> pdb=" O PHE B 812 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B 799 " --> pdb=" O HIS B 922 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS B 922 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYS B 877 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 876 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 369 " --> pdb=" O VAL B 876 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU B 878 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU C 367 " --> pdb=" O GLU B 878 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY B 880 " --> pdb=" O CYS C 365 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N CYS C 365 " --> pdb=" O GLY B 880 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU B 882 " --> pdb=" O ARG C 363 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ARG C 363 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE C 311 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 186 through 190 removed outlier: 6.876A pdb=" N LEU C 181 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA C 190 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 179 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASP D 52 " --> pdb=" O MET D 109 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ARG D 111 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA D 54 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU D 113 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR D 56 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TRP D 115 " --> pdb=" O TYR D 56 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE D 58 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N ALA D 138 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS D 57 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU D 140 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE D 59 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU D 142 " --> pdb=" O PHE D 59 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER D 61 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N SER D 144 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 29 through 30 663 hydrogen bonds defined for protein. 1857 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: 8.54 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 13326 1.13 - 1.30: 2166 1.30 - 1.48: 5499 1.48 - 1.65: 5823 1.65 - 1.82: 102 Bond restraints: 26916 Sorted by residual: bond pdb=" NE1 TRP D 15 " pdb=" HE1 TRP D 15 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" CD1 PHE A 400 " pdb=" HD1 PHE A 400 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" CD2 PHE A 100 " pdb=" HD2 PHE A 100 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.85e+01 bond pdb=" NE ARG A 348 " pdb=" HE ARG A 348 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" CD1 PHE D 145 " pdb=" HD1 PHE D 145 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.78e+01 ... (remaining 26911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 43786 2.70 - 5.41: 3542 5.41 - 8.11: 1396 8.11 - 10.82: 11 10.82 - 13.52: 43 Bond angle restraints: 48778 Sorted by residual: angle pdb=" C PHE B 570 " pdb=" N PRO B 571 " pdb=" CA PRO B 571 " ideal model delta sigma weight residual 120.21 128.43 -8.22 9.60e-01 1.09e+00 7.33e+01 angle pdb=" C GLY A 188 " pdb=" N PRO A 189 " pdb=" CA PRO A 189 " ideal model delta sigma weight residual 120.03 128.29 -8.26 9.90e-01 1.02e+00 6.95e+01 angle pdb=" C GLN A 264 " pdb=" N PRO A 265 " pdb=" CA PRO A 265 " ideal model delta sigma weight residual 119.56 127.66 -8.10 1.01e+00 9.80e-01 6.43e+01 angle pdb=" C GLY B 655 " pdb=" N PRO B 656 " pdb=" CA PRO B 656 " ideal model delta sigma weight residual 120.03 127.48 -7.45 9.90e-01 1.02e+00 5.66e+01 angle pdb=" C VAL D 185 " pdb=" N PRO D 186 " pdb=" CA PRO D 186 " ideal model delta sigma weight residual 119.85 127.36 -7.51 1.01e+00 9.80e-01 5.53e+01 ... (remaining 48773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 12222 32.94 - 65.88: 381 65.88 - 98.82: 17 98.82 - 131.76: 1 131.76 - 164.70: 4 Dihedral angle restraints: 12625 sinusoidal: 6923 harmonic: 5702 Sorted by residual: dihedral pdb=" O3B GTP D 301 " pdb=" O3A GTP D 301 " pdb=" PB GTP D 301 " pdb=" PA GTP D 301 " ideal model delta sinusoidal sigma weight residual -68.92 95.78 -164.70 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C5' GTP D 301 " pdb=" O5' GTP D 301 " pdb=" PA GTP D 301 " pdb=" O3A GTP D 301 " ideal model delta sinusoidal sigma weight residual 69.27 -80.66 149.93 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" C8 GTP D 301 " pdb=" C1' GTP D 301 " pdb=" N9 GTP D 301 " pdb=" O4' GTP D 301 " ideal model delta sinusoidal sigma weight residual 104.59 -33.30 137.89 1 2.00e+01 2.50e-03 4.18e+01 ... (remaining 12622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1493 0.072 - 0.145: 499 0.145 - 0.217: 96 0.217 - 0.289: 15 0.289 - 0.361: 6 Chirality restraints: 2109 Sorted by residual: chirality pdb=" CA PHE A 401 " pdb=" N PHE A 401 " pdb=" C PHE A 401 " pdb=" CB PHE A 401 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA LEU A 138 " pdb=" N LEU A 138 " pdb=" C LEU A 138 " pdb=" CB LEU A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA TRP A 90 " pdb=" N TRP A 90 " pdb=" C TRP A 90 " pdb=" CB TRP A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 2106 not shown) Planarity restraints: 3894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 90 " 0.177 2.00e-02 2.50e+03 5.74e-02 1.32e+02 pdb=" CG TRP A 90 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 90 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A 90 " -0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP A 90 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TRP A 90 " -0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP A 90 " -0.046 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 90 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 90 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP A 90 " 0.025 2.00e-02 2.50e+03 pdb=" HD1 TRP A 90 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP A 90 " -0.011 2.00e-02 2.50e+03 pdb=" HE3 TRP A 90 " -0.057 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 90 " 0.056 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 90 " -0.013 2.00e-02 2.50e+03 pdb=" HH2 TRP A 90 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 845 " -0.122 2.00e-02 2.50e+03 4.78e-02 6.85e+01 pdb=" CG PHE B 845 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 845 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE B 845 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 PHE B 845 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE B 845 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE B 845 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 PHE B 845 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE B 845 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 PHE B 845 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE B 845 " -0.010 2.00e-02 2.50e+03 pdb=" HZ PHE B 845 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 27 " 0.103 2.00e-02 2.50e+03 4.29e-02 5.51e+01 pdb=" CG TYR A 27 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 27 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 27 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 27 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A 27 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR A 27 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 27 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 TYR A 27 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 TYR A 27 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 TYR A 27 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 27 " -0.009 2.00e-02 2.50e+03 ... (remaining 3891 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2488 2.20 - 2.80: 53571 2.80 - 3.40: 75584 3.40 - 4.00: 102804 4.00 - 4.60: 154368 Nonbonded interactions: 388815 Sorted by model distance: nonbonded pdb="HG23 THR C 237 " pdb=" HG CYS C 247 " model vdw 1.600 2.440 nonbonded pdb=" O TYR D 24 " pdb=" HG CYS D 27 " model vdw 1.652 2.620 nonbonded pdb=" O PRO C 274 " pdb=" HG CYS C 278 " model vdw 1.670 2.620 nonbonded pdb=" O ASP B 423 " pdb=" HG CYS B 427 " model vdw 1.673 2.620 nonbonded pdb=" O THR C 239 " pdb=" H LEU D 39 " model vdw 1.693 2.450 ... (remaining 388810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.49 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.160 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 28.630 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 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:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.013 0.100 13548 Z= 0.723 Angle : 1.334 11.796 18387 Z= 0.898 Chirality : 0.074 0.361 2109 Planarity : 0.013 0.071 2326 Dihedral : 12.612 164.700 4998 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1640 helix: -1.72 (0.16), residues: 521 sheet: 1.75 (0.25), residues: 382 loop : 1.57 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 593 TYR 0.094 0.014 TYR A 27 PHE 0.079 0.009 PHE B 845 TRP 0.121 0.014 TRP A 90 HIS 0.011 0.002 HIS C 341 Details of bonding type rmsd covalent geometry : bond 0.01313 (13548) covalent geometry : angle 1.33434 (18387) hydrogen bonds : bond 0.18763 ( 659) hydrogen bonds : angle 7.54445 ( 1857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ILE cc_start: 0.8950 (mm) cc_final: 0.8706 (mt) REVERT: D 16 HIS cc_start: 0.8453 (p-80) cc_final: 0.8241 (p90) REVERT: D 157 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7990 (mm110) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2718 time to fit residues: 116.3402 Evaluate side-chains 179 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 848 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.089772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071282 restraints weight = 136621.068| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 5.01 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13548 Z= 0.152 Angle : 0.657 6.206 18387 Z= 0.360 Chirality : 0.042 0.173 2109 Planarity : 0.006 0.049 2326 Dihedral : 9.218 168.463 1810 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.22 % Favored : 98.66 % Rotamer: Outliers : 1.16 % Allowed : 7.51 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.20), residues: 1640 helix: 0.51 (0.20), residues: 541 sheet: 1.18 (0.25), residues: 374 loop : 0.87 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 186 TYR 0.020 0.002 TYR B 902 PHE 0.024 0.002 PHE B 845 TRP 0.020 0.002 TRP A 90 HIS 0.013 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00312 (13548) covalent geometry : angle 0.65666 (18387) hydrogen bonds : bond 0.06095 ( 659) hydrogen bonds : angle 6.28411 ( 1857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8245 (tptt) REVERT: A 488 GLN cc_start: 0.9081 (mp10) cc_final: 0.8768 (mp10) REVERT: B 516 TYR cc_start: 0.7352 (m-80) cc_final: 0.7037 (m-80) REVERT: B 831 LEU cc_start: 0.8316 (mp) cc_final: 0.7978 (tp) outliers start: 17 outliers final: 12 residues processed: 211 average time/residue: 0.2640 time to fit residues: 80.9765 Evaluate side-chains 171 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 15 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 10 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN B 428 GLN B 562 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.086768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068271 restraints weight = 140007.457| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 5.00 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13548 Z= 0.230 Angle : 0.632 6.566 18387 Z= 0.341 Chirality : 0.041 0.150 2109 Planarity : 0.005 0.051 2326 Dihedral : 8.687 160.610 1810 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.57 % Allowed : 8.60 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1640 helix: 1.17 (0.21), residues: 551 sheet: 0.34 (0.25), residues: 384 loop : 0.56 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 513 TYR 0.022 0.001 TYR B 902 PHE 0.012 0.002 PHE B 845 TRP 0.014 0.001 TRP A 90 HIS 0.018 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00484 (13548) covalent geometry : angle 0.63205 (18387) hydrogen bonds : bond 0.04974 ( 659) hydrogen bonds : angle 6.07520 ( 1857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8357 (tppt) REVERT: A 282 MET cc_start: 0.5070 (mtm) cc_final: 0.4442 (tpp) REVERT: A 303 ILE cc_start: 0.9068 (mm) cc_final: 0.8676 (mm) REVERT: A 488 GLN cc_start: 0.9155 (mp10) cc_final: 0.8789 (mp10) REVERT: B 831 LEU cc_start: 0.8387 (mp) cc_final: 0.8083 (tp) REVERT: D 231 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8693 (mp) outliers start: 23 outliers final: 16 residues processed: 182 average time/residue: 0.2708 time to fit residues: 71.0847 Evaluate side-chains 168 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 231 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 165 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 0.0170 chunk 91 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 overall best weight: 1.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.087527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069260 restraints weight = 137985.405| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.91 r_work: 0.3196 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13548 Z= 0.131 Angle : 0.564 5.353 18387 Z= 0.294 Chirality : 0.040 0.148 2109 Planarity : 0.004 0.057 2326 Dihedral : 8.433 176.945 1810 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.16 % Allowed : 9.42 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.20), residues: 1640 helix: 1.55 (0.22), residues: 543 sheet: 0.22 (0.25), residues: 387 loop : 0.39 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 119 TYR 0.016 0.001 TYR B 902 PHE 0.009 0.001 PHE B 883 TRP 0.012 0.001 TRP C 268 HIS 0.008 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00284 (13548) covalent geometry : angle 0.56407 (18387) hydrogen bonds : bond 0.04193 ( 659) hydrogen bonds : angle 5.77381 ( 1857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8389 (tppt) REVERT: B 410 ASP cc_start: 0.9166 (t70) cc_final: 0.8935 (t0) REVERT: B 831 LEU cc_start: 0.8379 (mp) cc_final: 0.8112 (tp) outliers start: 17 outliers final: 16 residues processed: 181 average time/residue: 0.2655 time to fit residues: 70.5202 Evaluate side-chains 168 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.088170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069762 restraints weight = 137781.628| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 4.93 r_work: 0.3211 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13548 Z= 0.112 Angle : 0.538 6.777 18387 Z= 0.277 Chirality : 0.040 0.175 2109 Planarity : 0.004 0.054 2326 Dihedral : 8.051 170.323 1810 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.16 % Allowed : 10.31 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.21), residues: 1640 helix: 1.81 (0.23), residues: 543 sheet: 0.16 (0.25), residues: 393 loop : 0.43 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 307 TYR 0.015 0.001 TYR B 902 PHE 0.008 0.001 PHE A 401 TRP 0.010 0.001 TRP A 90 HIS 0.003 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00242 (13548) covalent geometry : angle 0.53818 (18387) hydrogen bonds : bond 0.03751 ( 659) hydrogen bonds : angle 5.56195 ( 1857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TRP cc_start: 0.7391 (m100) cc_final: 0.6627 (m100) REVERT: A 93 LYS cc_start: 0.8979 (ttpt) cc_final: 0.7707 (tppt) REVERT: A 410 MET cc_start: 0.8667 (mtm) cc_final: 0.8378 (mtm) REVERT: B 410 ASP cc_start: 0.9167 (t70) cc_final: 0.8955 (t0) REVERT: B 831 LEU cc_start: 0.8334 (mp) cc_final: 0.8073 (tp) REVERT: D 231 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8729 (mp) outliers start: 17 outliers final: 14 residues processed: 174 average time/residue: 0.2735 time to fit residues: 69.3910 Evaluate side-chains 167 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 231 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 163 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 127 optimal weight: 0.0870 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.087882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.069442 restraints weight = 139439.844| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 4.95 r_work: 0.3196 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13548 Z= 0.123 Angle : 0.525 5.634 18387 Z= 0.272 Chirality : 0.040 0.144 2109 Planarity : 0.004 0.054 2326 Dihedral : 7.959 173.438 1810 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.16 % Allowed : 10.72 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.21), residues: 1640 helix: 1.82 (0.22), residues: 551 sheet: 0.18 (0.25), residues: 392 loop : 0.39 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 119 TYR 0.015 0.001 TYR B 902 PHE 0.010 0.001 PHE A 560 TRP 0.011 0.001 TRP C 268 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00266 (13548) covalent geometry : angle 0.52541 (18387) hydrogen bonds : bond 0.03644 ( 659) hydrogen bonds : angle 5.50597 ( 1857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8370 (tppt) REVERT: A 565 ASP cc_start: 0.9336 (m-30) cc_final: 0.8891 (t70) REVERT: B 410 ASP cc_start: 0.9162 (t70) cc_final: 0.8954 (t0) REVERT: B 831 LEU cc_start: 0.8341 (mp) cc_final: 0.8077 (tp) outliers start: 17 outliers final: 14 residues processed: 174 average time/residue: 0.2686 time to fit residues: 68.9946 Evaluate side-chains 168 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 119 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.086875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068384 restraints weight = 139462.342| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 4.97 r_work: 0.3182 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13548 Z= 0.152 Angle : 0.539 5.875 18387 Z= 0.280 Chirality : 0.040 0.150 2109 Planarity : 0.004 0.054 2326 Dihedral : 7.800 175.485 1810 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.43 % Allowed : 10.99 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.21), residues: 1640 helix: 1.86 (0.22), residues: 550 sheet: 0.03 (0.26), residues: 388 loop : 0.29 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 405 TYR 0.016 0.001 TYR B 902 PHE 0.014 0.001 PHE A 560 TRP 0.010 0.001 TRP C 268 HIS 0.004 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00329 (13548) covalent geometry : angle 0.53876 (18387) hydrogen bonds : bond 0.03646 ( 659) hydrogen bonds : angle 5.52529 ( 1857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.9055 (ttpt) cc_final: 0.8417 (tppt) REVERT: B 831 LEU cc_start: 0.8355 (mp) cc_final: 0.8088 (tp) outliers start: 21 outliers final: 18 residues processed: 169 average time/residue: 0.2496 time to fit residues: 62.6584 Evaluate side-chains 165 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 87 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.086431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067954 restraints weight = 140062.568| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 4.99 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13548 Z= 0.161 Angle : 0.550 8.164 18387 Z= 0.285 Chirality : 0.040 0.141 2109 Planarity : 0.004 0.054 2326 Dihedral : 7.638 174.090 1810 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.64 % Allowed : 11.40 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1640 helix: 1.84 (0.22), residues: 544 sheet: -0.08 (0.26), residues: 383 loop : 0.19 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 525 TYR 0.015 0.001 TYR B 902 PHE 0.012 0.001 PHE B 883 TRP 0.009 0.001 TRP C 268 HIS 0.004 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00352 (13548) covalent geometry : angle 0.54962 (18387) hydrogen bonds : bond 0.03649 ( 659) hydrogen bonds : angle 5.55712 ( 1857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TRP cc_start: 0.7494 (m100) cc_final: 0.6769 (m100) REVERT: A 93 LYS cc_start: 0.9029 (ttpt) cc_final: 0.7813 (tppt) REVERT: A 558 LYS cc_start: 0.9233 (mppt) cc_final: 0.8991 (mmtp) REVERT: B 831 LEU cc_start: 0.8336 (mp) cc_final: 0.8041 (tp) REVERT: C 77 ASP cc_start: 0.8499 (p0) cc_final: 0.8160 (m-30) REVERT: C 245 GLU cc_start: 0.8603 (pm20) cc_final: 0.8202 (pm20) outliers start: 24 outliers final: 21 residues processed: 164 average time/residue: 0.2503 time to fit residues: 60.9369 Evaluate side-chains 161 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 22 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.084355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066022 restraints weight = 141850.413| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.87 r_work: 0.3123 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13548 Z= 0.253 Angle : 0.606 6.954 18387 Z= 0.319 Chirality : 0.041 0.139 2109 Planarity : 0.005 0.052 2326 Dihedral : 7.710 171.331 1810 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.50 % Allowed : 11.60 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1640 helix: 1.58 (0.22), residues: 544 sheet: -0.30 (0.26), residues: 379 loop : -0.04 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 326 TYR 0.019 0.002 TYR B 902 PHE 0.015 0.002 PHE B 883 TRP 0.013 0.002 TRP D 97 HIS 0.007 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00547 (13548) covalent geometry : angle 0.60601 (18387) hydrogen bonds : bond 0.04050 ( 659) hydrogen bonds : angle 5.84653 ( 1857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TRP cc_start: 0.7830 (m100) cc_final: 0.6827 (m100) REVERT: A 93 LYS cc_start: 0.9197 (ttpt) cc_final: 0.8048 (tppt) REVERT: B 831 LEU cc_start: 0.8476 (mp) cc_final: 0.8155 (tp) REVERT: C 77 ASP cc_start: 0.8778 (p0) cc_final: 0.8277 (m-30) REVERT: C 245 GLU cc_start: 0.8757 (pm20) cc_final: 0.8416 (pm20) outliers start: 22 outliers final: 19 residues processed: 157 average time/residue: 0.2501 time to fit residues: 58.8392 Evaluate side-chains 155 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 13 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.085518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.067075 restraints weight = 139957.339| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.97 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13548 Z= 0.155 Angle : 0.563 11.490 18387 Z= 0.289 Chirality : 0.041 0.141 2109 Planarity : 0.004 0.054 2326 Dihedral : 7.572 172.341 1810 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 1.02 % Allowed : 12.22 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.21), residues: 1640 helix: 1.72 (0.23), residues: 548 sheet: -0.28 (0.26), residues: 376 loop : -0.01 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 525 TYR 0.015 0.001 TYR B 902 PHE 0.015 0.001 PHE A 560 TRP 0.010 0.001 TRP D 115 HIS 0.004 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00338 (13548) covalent geometry : angle 0.56259 (18387) hydrogen bonds : bond 0.03754 ( 659) hydrogen bonds : angle 5.69572 ( 1857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TRP cc_start: 0.7655 (m100) cc_final: 0.6664 (m100) REVERT: A 93 LYS cc_start: 0.9091 (ttpt) cc_final: 0.7865 (tppt) REVERT: A 565 ASP cc_start: 0.9329 (m-30) cc_final: 0.8962 (t70) REVERT: B 502 PHE cc_start: 0.8625 (m-10) cc_final: 0.8425 (m-10) REVERT: B 831 LEU cc_start: 0.8343 (mp) cc_final: 0.8052 (tp) REVERT: C 77 ASP cc_start: 0.8541 (p0) cc_final: 0.8139 (m-30) REVERT: C 245 GLU cc_start: 0.8549 (pm20) cc_final: 0.8153 (pm20) REVERT: D 230 VAL cc_start: 0.8929 (m) cc_final: 0.8654 (p) outliers start: 15 outliers final: 13 residues processed: 155 average time/residue: 0.2514 time to fit residues: 58.0638 Evaluate side-chains 149 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 129 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.086128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.067728 restraints weight = 141173.405| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 4.92 r_work: 0.3156 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13548 Z= 0.141 Angle : 0.557 11.158 18387 Z= 0.285 Chirality : 0.041 0.144 2109 Planarity : 0.004 0.055 2326 Dihedral : 7.442 172.373 1810 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 1.02 % Allowed : 12.63 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.21), residues: 1640 helix: 1.81 (0.23), residues: 548 sheet: -0.22 (0.26), residues: 377 loop : -0.01 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 525 TYR 0.014 0.001 TYR B 902 PHE 0.019 0.001 PHE A 560 TRP 0.011 0.001 TRP D 97 HIS 0.004 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00308 (13548) covalent geometry : angle 0.55682 (18387) hydrogen bonds : bond 0.03617 ( 659) hydrogen bonds : angle 5.61924 ( 1857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4177.14 seconds wall clock time: 71 minutes 50.81 seconds (4310.81 seconds total)