Starting phenix.real_space_refine on Wed Feb 4 18:09:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qks_53220/02_2026/9qks_53220.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qks_53220/02_2026/9qks_53220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qks_53220/02_2026/9qks_53220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qks_53220/02_2026/9qks_53220.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qks_53220/02_2026/9qks_53220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qks_53220/02_2026/9qks_53220.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 7634 2.51 5 N 2029 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11940 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "C" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1814 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 212} Chain: "D" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1814 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain: "G" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 3018 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 12, 'TRANS': 343} Chain breaks: 1 Chain: "H" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4656 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 23, 'TRANS': 540} Chain breaks: 3 Time building chain proxies: 2.23, per 1000 atoms: 0.19 Number of scatterers: 11940 At special positions: 0 Unit cell: (110.4, 133.2, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 2250 8.00 N 2029 7.00 C 7634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 68 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 396.8 milliseconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2770 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 19 sheets defined 39.7% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 26 through 39 removed outlier: 3.620A pdb=" N VAL A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 14 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 38 through 47 removed outlier: 3.630A pdb=" N VAL C 43 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 47 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.533A pdb=" N LYS C 79 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 80 " --> pdb=" O PHE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 98 removed outlier: 3.642A pdb=" N LYS C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 140 through 156 removed outlier: 3.561A pdb=" N ALA C 149 " --> pdb=" O GLN C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 167 removed outlier: 3.929A pdb=" N TYR C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 165 " --> pdb=" O PHE C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.538A pdb=" N THR C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'D' and resid 9 through 14 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.954A pdb=" N VAL D 43 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 47 " --> pdb=" O ILE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.542A pdb=" N LYS D 79 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 80 " --> pdb=" O PHE D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.627A pdb=" N VAL D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 113 Processing helix chain 'D' and resid 139 through 156 removed outlier: 3.892A pdb=" N ALA D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 166 removed outlier: 3.763A pdb=" N TYR D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 165 " --> pdb=" O PHE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 185 through 204 removed outlier: 3.566A pdb=" N HIS D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 222 removed outlier: 3.692A pdb=" N TYR D 220 " --> pdb=" O ASN D 216 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY D 222 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 223 Processing helix chain 'G' and resid 304 through 346 removed outlier: 3.812A pdb=" N GLN G 308 " --> pdb=" O ARG G 304 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS G 311 " --> pdb=" O ASN G 307 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG G 312 " --> pdb=" O GLN G 308 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU G 314 " --> pdb=" O LYS G 310 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS G 315 " --> pdb=" O LYS G 311 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL G 319 " --> pdb=" O LYS G 315 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR G 320 " --> pdb=" O ARG G 316 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU G 331 " --> pdb=" O LYS G 327 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN G 332 " --> pdb=" O ARG G 328 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA G 333 " --> pdb=" O LYS G 329 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G 334 " --> pdb=" O GLU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 348 through 358 removed outlier: 3.598A pdb=" N GLU G 358 " --> pdb=" O TYR G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 415 removed outlier: 5.011A pdb=" N SER G 408 " --> pdb=" O LEU G 404 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN G 409 " --> pdb=" O MET G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 456 removed outlier: 3.552A pdb=" N ILE G 445 " --> pdb=" O VAL G 441 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS G 446 " --> pdb=" O LYS G 442 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN G 447 " --> pdb=" O ASN G 443 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE G 454 " --> pdb=" O GLY G 450 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE G 455 " --> pdb=" O GLN G 451 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN G 456 " --> pdb=" O LEU G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 468 through 472 removed outlier: 3.541A pdb=" N GLU G 471 " --> pdb=" O HIS G 468 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR G 472 " --> pdb=" O GLU G 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 468 through 472' Processing helix chain 'G' and resid 473 through 481 removed outlier: 4.460A pdb=" N TRP G 477 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP G 480 " --> pdb=" O TRP G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 517 removed outlier: 4.975A pdb=" N SER G 506 " --> pdb=" O ASP G 502 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER G 507 " --> pdb=" O GLN G 503 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 508 " --> pdb=" O LEU G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 541 Processing helix chain 'G' and resid 545 through 551 Processing helix chain 'G' and resid 553 through 557 Processing helix chain 'G' and resid 566 through 570 Processing helix chain 'G' and resid 609 through 620 removed outlier: 3.757A pdb=" N LEU G 620 " --> pdb=" O THR G 616 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 137 removed outlier: 3.725A pdb=" N PHE H 137 " --> pdb=" O PRO H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 222 removed outlier: 3.635A pdb=" N LYS H 221 " --> pdb=" O THR H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 346 removed outlier: 3.919A pdb=" N ARG H 309 " --> pdb=" O ASP H 305 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS H 310 " --> pdb=" O LYS H 306 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS H 311 " --> pdb=" O ASN H 307 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ARG H 312 " --> pdb=" O GLN H 308 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU H 313 " --> pdb=" O ARG H 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE H 346 " --> pdb=" O LEU H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 359 removed outlier: 3.528A pdb=" N GLU H 358 " --> pdb=" O TYR H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 399 removed outlier: 3.689A pdb=" N ASN H 398 " --> pdb=" O ASP H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 415 removed outlier: 3.705A pdb=" N VAL H 414 " --> pdb=" O HIS H 410 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR H 415 " --> pdb=" O MET H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 455 removed outlier: 4.499A pdb=" N HIS H 446 " --> pdb=" O LYS H 442 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLN H 447 " --> pdb=" O ASN H 443 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU H 448 " --> pdb=" O GLU H 444 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE H 455 " --> pdb=" O GLN H 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 471 through 476 Processing helix chain 'H' and resid 477 through 481 removed outlier: 3.927A pdb=" N TRP H 480 " --> pdb=" O TRP H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 517 removed outlier: 4.278A pdb=" N SER H 506 " --> pdb=" O ASP H 502 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER H 507 " --> pdb=" O GLN H 503 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU H 514 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG H 515 " --> pdb=" O LEU H 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 518 through 522 removed outlier: 3.601A pdb=" N LYS H 521 " --> pdb=" O GLU H 518 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU H 522 " --> pdb=" O ASP H 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 518 through 522' Processing helix chain 'H' and resid 545 through 550 Processing helix chain 'H' and resid 553 through 556 Processing helix chain 'H' and resid 566 through 570 Processing helix chain 'H' and resid 609 through 620 removed outlier: 4.102A pdb=" N LEU H 620 " --> pdb=" O THR H 616 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 removed outlier: 8.972A pdb=" N LEU A 76 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR A 6 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE A 78 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP A 8 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 17 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP A 18 " --> pdb=" O VAL H 922 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL H 922 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY H 926 " --> pdb=" O THR H 923 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 16 through 20 removed outlier: 3.629A pdb=" N ILE C 63 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP C 56 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 52 " --> pdb=" O GLN C 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 73 through 74 removed outlier: 3.618A pdb=" N LYS C 73 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 105 through 106 removed outlier: 3.618A pdb=" N ASN C 106 " --> pdb=" O GLY C 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 207 through 211 Processing sheet with id=AA6, first strand: chain 'D' and resid 16 through 18 removed outlier: 3.657A pdb=" N VAL D 16 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU D 18 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS D 52 " --> pdb=" O GLN D 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 73 through 74 Processing sheet with id=AA8, first strand: chain 'D' and resid 105 through 106 Processing sheet with id=AA9, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AB1, first strand: chain 'G' and resid 375 through 384 removed outlier: 5.405A pdb=" N ARG G 377 " --> pdb=" O VAL G 425 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL G 425 " --> pdb=" O ARG G 377 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY G 379 " --> pdb=" O VAL G 423 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL G 383 " --> pdb=" O ARG G 419 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ARG G 419 " --> pdb=" O VAL G 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 461 through 466 removed outlier: 6.644A pdb=" N VAL G 435 " --> pdb=" O TYR G 580 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU G 577 " --> pdb=" O LEU G 589 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLU G 585 " --> pdb=" O PHE G 600 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE G 600 " --> pdb=" O GLU G 585 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP G 587 " --> pdb=" O ILE G 598 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE G 598 " --> pdb=" O ASP G 587 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU G 589 " --> pdb=" O VAL G 596 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 22 through 24 removed outlier: 3.719A pdb=" N ILE H 100 " --> pdb=" O TRP H 16 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE H 18 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 47 through 48 removed outlier: 3.620A pdb=" N VAL H 37 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL H 72 " --> pdb=" O LEU H 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 168 through 169 removed outlier: 3.698A pdb=" N HIS H 201 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR H 210 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 130 through 131 removed outlier: 3.583A pdb=" N ILE H 130 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR H 144 " --> pdb=" O GLU H 159 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU H 159 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER H 146 " --> pdb=" O ARG H 157 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 240 through 242 Processing sheet with id=AB8, first strand: chain 'H' and resid 375 through 384 removed outlier: 7.016A pdb=" N VAL H 423 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR H 380 " --> pdb=" O ALA H 421 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA H 421 " --> pdb=" O THR H 380 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR H 382 " --> pdb=" O ARG H 419 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG H 419 " --> pdb=" O THR H 382 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP H 417 " --> pdb=" O PRO H 384 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 432 through 435 removed outlier: 6.855A pdb=" N ARG H 462 " --> pdb=" O VAL H 531 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL H 533 " --> pdb=" O ARG H 462 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL H 464 " --> pdb=" O VAL H 533 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 576 through 580 removed outlier: 6.543A pdb=" N LEU H 577 " --> pdb=" O LEU H 589 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU H 589 " --> pdb=" O LEU H 577 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU H 585 " --> pdb=" O PHE H 600 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE H 600 " --> pdb=" O GLU H 585 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP H 587 " --> pdb=" O ILE H 598 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE H 598 " --> pdb=" O ASP H 587 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU H 589 " --> pdb=" O VAL H 596 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL H 596 " --> pdb=" O LEU H 589 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3922 1.34 - 1.46: 2643 1.46 - 1.58: 5589 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12204 Sorted by residual: bond pdb=" N LEU H 14 " pdb=" CA LEU H 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N GLN D 5 " pdb=" CA GLN D 5 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N GLN C 5 " pdb=" CA GLN C 5 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N THR G 217 " pdb=" CA THR G 217 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 ... (remaining 12199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 15111 0.94 - 1.89: 1109 1.89 - 2.83: 170 2.83 - 3.77: 70 3.77 - 4.71: 15 Bond angle restraints: 16475 Sorted by residual: angle pdb=" N GLN H 537 " pdb=" CA GLN H 537 " pdb=" C GLN H 537 " ideal model delta sigma weight residual 110.24 105.74 4.50 1.47e+00 4.63e-01 9.38e+00 angle pdb=" CA VAL H 383 " pdb=" C VAL H 383 " pdb=" N PRO H 384 " ideal model delta sigma weight residual 116.57 119.27 -2.70 9.80e-01 1.04e+00 7.60e+00 angle pdb=" N PRO D 134 " pdb=" CA PRO D 134 " pdb=" C PRO D 134 " ideal model delta sigma weight residual 110.70 113.50 -2.80 1.22e+00 6.72e-01 5.28e+00 angle pdb=" C TYR G 496 " pdb=" CA TYR G 496 " pdb=" CB TYR G 496 " ideal model delta sigma weight residual 111.03 106.77 4.26 1.87e+00 2.86e-01 5.19e+00 angle pdb=" C ILE D 133 " pdb=" CA ILE D 133 " pdb=" CB ILE D 133 " ideal model delta sigma weight residual 109.89 112.32 -2.43 1.08e+00 8.57e-01 5.05e+00 ... (remaining 16470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6576 17.85 - 35.70: 632 35.70 - 53.54: 135 53.54 - 71.39: 40 71.39 - 89.24: 18 Dihedral angle restraints: 7401 sinusoidal: 3137 harmonic: 4264 Sorted by residual: dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 68 " pdb=" CB CYS A 68 " ideal model delta sinusoidal sigma weight residual 93.00 155.18 -62.18 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CA ILE D 133 " pdb=" C ILE D 133 " pdb=" N PRO D 134 " pdb=" CA PRO D 134 " ideal model delta harmonic sigma weight residual -180.00 -153.42 -26.58 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA CYS A 63 " pdb=" C CYS A 63 " pdb=" N LYS A 64 " pdb=" CA LYS A 64 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 7398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1084 0.029 - 0.059: 470 0.059 - 0.088: 89 0.088 - 0.117: 100 0.117 - 0.146: 34 Chirality restraints: 1777 Sorted by residual: chirality pdb=" CA ILE G 561 " pdb=" N ILE G 561 " pdb=" C ILE G 561 " pdb=" CB ILE G 561 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE H 928 " pdb=" N ILE H 928 " pdb=" C ILE H 928 " pdb=" CB ILE H 928 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE H 52 " pdb=" N ILE H 52 " pdb=" C ILE H 52 " pdb=" CB ILE H 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 1774 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 76 " 0.214 9.50e-02 1.11e+02 9.59e-02 6.01e+00 pdb=" NE ARG D 76 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 76 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 76 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 76 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 88 " -0.010 2.00e-02 2.50e+03 1.16e-02 2.34e+00 pdb=" CG PHE H 88 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE H 88 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE H 88 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE H 88 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 88 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE H 88 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 42 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 43 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.021 5.00e-02 4.00e+02 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 212 2.66 - 3.22: 11273 3.22 - 3.78: 15724 3.78 - 4.34: 21285 4.34 - 4.90: 35426 Nonbonded interactions: 83920 Sorted by model distance: nonbonded pdb=" OD1 ASN C 101 " pdb=" N LEU C 102 " model vdw 2.101 3.120 nonbonded pdb=" N GLU D 10 " pdb=" OE1 GLU D 10 " model vdw 2.123 3.120 nonbonded pdb=" OG SER H 571 " pdb=" OD1 ASN H 573 " model vdw 2.159 3.040 nonbonded pdb=" N GLN H 142 " pdb=" OE1 GLN H 142 " model vdw 2.178 3.120 nonbonded pdb=" O GLU G 550 " pdb=" ND2 ASN G 573 " model vdw 2.190 3.120 ... (remaining 83915 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12205 Z= 0.165 Angle : 0.576 4.714 16477 Z= 0.335 Chirality : 0.042 0.146 1777 Planarity : 0.004 0.096 2130 Dihedral : 15.589 89.241 4628 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 0.99 % Allowed : 12.41 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.90 (0.22), residues: 1423 helix: 0.27 (0.25), residues: 468 sheet: -1.09 (0.32), residues: 253 loop : -0.92 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 76 TYR 0.015 0.002 TYR H 496 PHE 0.027 0.002 PHE H 88 TRP 0.007 0.001 TRP G 480 HIS 0.007 0.001 HIS H 446 Details of bonding type rmsd covalent geometry : bond 0.00353 (12204) covalent geometry : angle 0.57631 (16475) SS BOND : bond 0.00740 ( 1) SS BOND : angle 1.13504 ( 2) hydrogen bonds : bond 0.23282 ( 456) hydrogen bonds : angle 6.53962 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.8340 (p90) cc_final: 0.8072 (p90) REVERT: A 18 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7836 (p0) outliers start: 13 outliers final: 8 residues processed: 125 average time/residue: 0.1129 time to fit residues: 19.7634 Evaluate side-chains 83 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain G residue 453 SER Chi-restraints excluded: chain G residue 457 SER Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 195 ASP Chi-restraints excluded: chain H residue 367 SER Chi-restraints excluded: chain H residue 373 TYR Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain H residue 919 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN D 209 HIS H 188 GLN H 398 ASN H 446 HIS H 553 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.061669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.045089 restraints weight = 52470.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.046817 restraints weight = 28109.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.047960 restraints weight = 19250.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.048734 restraints weight = 15087.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.049254 restraints weight = 12834.887| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12205 Z= 0.124 Angle : 0.579 7.417 16477 Z= 0.311 Chirality : 0.044 0.166 1777 Planarity : 0.003 0.039 2130 Dihedral : 5.284 41.871 1586 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.33 % Rotamer: Outliers : 1.14 % Allowed : 14.01 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.08 (0.23), residues: 1423 helix: 1.00 (0.26), residues: 468 sheet: -0.04 (0.32), residues: 247 loop : -0.74 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 76 TYR 0.012 0.001 TYR H 202 PHE 0.010 0.001 PHE C 167 TRP 0.010 0.001 TRP D 144 HIS 0.004 0.001 HIS G 488 Details of bonding type rmsd covalent geometry : bond 0.00264 (12204) covalent geometry : angle 0.57885 (16475) SS BOND : bond 0.00669 ( 1) SS BOND : angle 0.83849 ( 2) hydrogen bonds : bond 0.05223 ( 456) hydrogen bonds : angle 4.69767 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.9444 (t0) cc_final: 0.9200 (t0) REVERT: A 18 ASP cc_start: 0.8745 (m-30) cc_final: 0.8177 (p0) REVERT: A 64 LYS cc_start: 0.9510 (ttmm) cc_final: 0.9175 (mmmt) REVERT: G 232 MET cc_start: 0.7731 (tpp) cc_final: 0.7502 (tpp) REVERT: G 417 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8879 (t70) REVERT: H 486 MET cc_start: 0.9419 (mmp) cc_final: 0.9179 (mmm) outliers start: 15 outliers final: 1 residues processed: 103 average time/residue: 0.0903 time to fit residues: 14.1342 Evaluate side-chains 65 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain G residue 417 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 86 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.044216 restraints weight = 53312.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.045896 restraints weight = 28639.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.047038 restraints weight = 19642.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.047805 restraints weight = 15407.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.048303 restraints weight = 13125.186| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12205 Z= 0.121 Angle : 0.523 7.382 16477 Z= 0.282 Chirality : 0.043 0.163 1777 Planarity : 0.003 0.036 2130 Dihedral : 4.643 22.480 1571 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 1.75 % Allowed : 13.79 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.24 (0.23), residues: 1423 helix: 1.17 (0.26), residues: 468 sheet: 0.37 (0.33), residues: 250 loop : -0.57 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 212 TYR 0.019 0.001 TYR H 202 PHE 0.012 0.001 PHE A 17 TRP 0.010 0.001 TRP D 87 HIS 0.004 0.001 HIS G 488 Details of bonding type rmsd covalent geometry : bond 0.00263 (12204) covalent geometry : angle 0.52316 (16475) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.94584 ( 2) hydrogen bonds : bond 0.04766 ( 456) hydrogen bonds : angle 4.39615 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.9449 (t0) cc_final: 0.9145 (t0) REVERT: A 10 LYS cc_start: 0.9263 (ptpp) cc_final: 0.9063 (ptpp) REVERT: A 18 ASP cc_start: 0.8868 (m-30) cc_final: 0.8584 (p0) REVERT: A 28 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8484 (ptmm) REVERT: A 62 GLU cc_start: 0.8576 (tp30) cc_final: 0.8342 (tp30) REVERT: A 77 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7963 (tm-30) REVERT: C 194 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8539 (tp40) REVERT: D 121 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8867 (p) REVERT: G 232 MET cc_start: 0.7787 (tpp) cc_final: 0.7528 (tpp) REVERT: G 417 ASP cc_start: 0.9238 (OUTLIER) cc_final: 0.8931 (t70) outliers start: 23 outliers final: 12 residues processed: 89 average time/residue: 0.0890 time to fit residues: 12.5280 Evaluate side-chains 75 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 596 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 424 THR Chi-restraints excluded: chain H residue 589 LEU Chi-restraints excluded: chain H residue 919 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 117 optimal weight: 0.0040 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN D 194 GLN G 248 GLN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 622 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.060187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.043635 restraints weight = 53409.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.045297 restraints weight = 28731.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.046422 restraints weight = 19757.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.047168 restraints weight = 15550.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.047660 restraints weight = 13274.805| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12205 Z= 0.125 Angle : 0.505 7.157 16477 Z= 0.269 Chirality : 0.042 0.158 1777 Planarity : 0.003 0.044 2130 Dihedral : 4.528 22.248 1571 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 2.36 % Allowed : 14.24 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.35 (0.23), residues: 1423 helix: 1.26 (0.26), residues: 468 sheet: 0.50 (0.33), residues: 254 loop : -0.55 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 212 TYR 0.018 0.001 TYR H 202 PHE 0.010 0.001 PHE H 465 TRP 0.011 0.001 TRP D 144 HIS 0.004 0.001 HIS G 488 Details of bonding type rmsd covalent geometry : bond 0.00280 (12204) covalent geometry : angle 0.50509 (16475) SS BOND : bond 0.00451 ( 1) SS BOND : angle 1.79360 ( 2) hydrogen bonds : bond 0.04436 ( 456) hydrogen bonds : angle 4.23999 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.9471 (t0) cc_final: 0.8998 (t0) REVERT: A 10 LYS cc_start: 0.9309 (ptpp) cc_final: 0.8901 (ptpp) REVERT: A 18 ASP cc_start: 0.9004 (m-30) cc_final: 0.8434 (p0) REVERT: A 77 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7892 (tm-30) REVERT: C 44 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8849 (mm) REVERT: C 45 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.8974 (mptt) REVERT: C 78 MET cc_start: 0.9214 (tpp) cc_final: 0.8984 (tpp) REVERT: C 194 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8549 (tp40) REVERT: D 121 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8897 (p) REVERT: G 219 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8077 (ptp) REVERT: G 232 MET cc_start: 0.7794 (tpp) cc_final: 0.7535 (tpp) REVERT: G 320 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.8244 (t80) REVERT: G 352 MET cc_start: 0.8676 (tpp) cc_final: 0.8414 (tpp) REVERT: G 417 ASP cc_start: 0.9217 (OUTLIER) cc_final: 0.8872 (t70) REVERT: H 444 GLU cc_start: 0.9249 (tp30) cc_final: 0.9035 (tp30) outliers start: 31 outliers final: 15 residues processed: 89 average time/residue: 0.0884 time to fit residues: 11.9911 Evaluate side-chains 82 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 320 TYR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 596 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 549 LEU Chi-restraints excluded: chain H residue 919 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.042338 restraints weight = 53898.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.043937 restraints weight = 29392.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.045007 restraints weight = 20454.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.045726 restraints weight = 16200.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.046199 restraints weight = 13901.795| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12205 Z= 0.173 Angle : 0.537 6.256 16477 Z= 0.286 Chirality : 0.043 0.147 1777 Planarity : 0.003 0.033 2130 Dihedral : 4.691 22.564 1571 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 2.74 % Allowed : 15.00 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.23), residues: 1423 helix: 1.23 (0.26), residues: 467 sheet: 0.43 (0.33), residues: 265 loop : -0.51 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 212 TYR 0.016 0.001 TYR H 202 PHE 0.014 0.001 PHE H 465 TRP 0.012 0.001 TRP D 144 HIS 0.004 0.001 HIS G 446 Details of bonding type rmsd covalent geometry : bond 0.00392 (12204) covalent geometry : angle 0.53696 (16475) SS BOND : bond 0.00007 ( 1) SS BOND : angle 1.93984 ( 2) hydrogen bonds : bond 0.04905 ( 456) hydrogen bonds : angle 4.40089 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 66 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.9431 (t0) cc_final: 0.8897 (t0) REVERT: A 10 LYS cc_start: 0.9309 (ptpp) cc_final: 0.8940 (ptpp) REVERT: A 18 ASP cc_start: 0.9134 (m-30) cc_final: 0.8433 (p0) REVERT: A 77 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8092 (tm-30) REVERT: C 44 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8864 (mm) REVERT: C 45 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.8957 (mptt) REVERT: C 194 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8544 (tp40) REVERT: G 219 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8141 (ptp) REVERT: G 232 MET cc_start: 0.7838 (tpp) cc_final: 0.7577 (tpp) REVERT: G 320 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.8099 (t80) REVERT: G 417 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8869 (t70) REVERT: H 555 HIS cc_start: 0.8787 (OUTLIER) cc_final: 0.8573 (p90) outliers start: 36 outliers final: 16 residues processed: 98 average time/residue: 0.0844 time to fit residues: 12.5028 Evaluate side-chains 79 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 320 TYR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 596 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 549 LEU Chi-restraints excluded: chain H residue 555 HIS Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 919 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- 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 = 0.3133 r_free = 0.3133 target = 0.059230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.042871 restraints weight = 53594.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.044481 restraints weight = 29280.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.045562 restraints weight = 20271.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.046290 restraints weight = 15999.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.046772 restraints weight = 13655.450| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12205 Z= 0.122 Angle : 0.507 8.555 16477 Z= 0.269 Chirality : 0.042 0.156 1777 Planarity : 0.003 0.039 2130 Dihedral : 4.530 22.485 1571 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 2.21 % Allowed : 16.22 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.23), residues: 1423 helix: 1.39 (0.26), residues: 468 sheet: 0.77 (0.34), residues: 253 loop : -0.49 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 212 TYR 0.015 0.001 TYR H 202 PHE 0.009 0.001 PHE H 465 TRP 0.009 0.001 TRP D 144 HIS 0.004 0.001 HIS G 488 Details of bonding type rmsd covalent geometry : bond 0.00272 (12204) covalent geometry : angle 0.50616 (16475) SS BOND : bond 0.00850 ( 1) SS BOND : angle 2.93097 ( 2) hydrogen bonds : bond 0.04290 ( 456) hydrogen bonds : angle 4.14750 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.9429 (t0) cc_final: 0.8918 (t0) REVERT: A 10 LYS cc_start: 0.9291 (ptpp) cc_final: 0.8893 (ptpp) REVERT: A 18 ASP cc_start: 0.9109 (m-30) cc_final: 0.8473 (p0) REVERT: C 44 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8866 (mm) REVERT: C 45 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.8948 (mptt) REVERT: C 194 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8556 (tp40) REVERT: G 219 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8213 (ptp) REVERT: G 232 MET cc_start: 0.7893 (tpp) cc_final: 0.7648 (tpp) REVERT: G 417 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8965 (t70) REVERT: H 555 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.8514 (p90) outliers start: 29 outliers final: 14 residues processed: 84 average time/residue: 0.0892 time to fit residues: 11.4863 Evaluate side-chains 78 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 596 VAL Chi-restraints excluded: chain H residue 345 HIS Chi-restraints excluded: chain H residue 549 LEU Chi-restraints excluded: chain H residue 555 HIS Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 919 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN C 126 HIS H 166 ASN H 555 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.041310 restraints weight = 54176.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.042853 restraints weight = 29952.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.043893 restraints weight = 20868.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.044560 restraints weight = 16564.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.045029 restraints weight = 14253.076| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12205 Z= 0.206 Angle : 0.576 7.816 16477 Z= 0.301 Chirality : 0.043 0.151 1777 Planarity : 0.004 0.058 2130 Dihedral : 4.837 22.824 1571 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 2.28 % Allowed : 16.30 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.23), residues: 1423 helix: 1.24 (0.26), residues: 467 sheet: 0.38 (0.32), residues: 276 loop : -0.54 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 212 TYR 0.015 0.001 TYR H 202 PHE 0.017 0.001 PHE H 465 TRP 0.010 0.001 TRP D 144 HIS 0.004 0.001 HIS G 446 Details of bonding type rmsd covalent geometry : bond 0.00466 (12204) covalent geometry : angle 0.57489 (16475) SS BOND : bond 0.00139 ( 1) SS BOND : angle 3.24048 ( 2) hydrogen bonds : bond 0.05013 ( 456) hydrogen bonds : angle 4.46098 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.9393 (t0) cc_final: 0.9022 (t0) REVERT: A 10 LYS cc_start: 0.9318 (ptpp) cc_final: 0.8957 (ptpp) REVERT: A 18 ASP cc_start: 0.9208 (m-30) cc_final: 0.8442 (p0) REVERT: C 44 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8849 (mm) REVERT: C 45 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.8955 (mptt) REVERT: C 194 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8574 (tp40) REVERT: G 219 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8259 (ptp) REVERT: G 232 MET cc_start: 0.7932 (tpp) cc_final: 0.7699 (tpp) REVERT: G 417 ASP cc_start: 0.9126 (OUTLIER) cc_final: 0.8812 (t70) REVERT: H 391 MET cc_start: 0.8781 (tpp) cc_final: 0.7894 (tpt) REVERT: H 444 GLU cc_start: 0.9282 (tp30) cc_final: 0.9073 (tp30) outliers start: 30 outliers final: 18 residues processed: 84 average time/residue: 0.0896 time to fit residues: 11.5233 Evaluate side-chains 77 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 424 THR Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 549 LEU Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 919 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 111 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 128 optimal weight: 0.2980 chunk 121 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN H 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.043856 restraints weight = 52344.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.045485 restraints weight = 28367.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.046592 restraints weight = 19540.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.047311 restraints weight = 15333.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.047817 restraints weight = 13084.493| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12205 Z= 0.093 Angle : 0.499 9.689 16477 Z= 0.262 Chirality : 0.042 0.144 1777 Planarity : 0.003 0.042 2130 Dihedral : 4.304 22.094 1571 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 1.83 % Allowed : 17.14 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.84 (0.23), residues: 1423 helix: 1.83 (0.26), residues: 451 sheet: 0.98 (0.33), residues: 256 loop : -0.42 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 212 TYR 0.010 0.001 TYR H 19 PHE 0.013 0.001 PHE H 18 TRP 0.010 0.001 TRP D 87 HIS 0.003 0.000 HIS G 488 Details of bonding type rmsd covalent geometry : bond 0.00194 (12204) covalent geometry : angle 0.49823 (16475) SS BOND : bond 0.00043 ( 1) SS BOND : angle 2.97285 ( 2) hydrogen bonds : bond 0.03639 ( 456) hydrogen bonds : angle 3.90068 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.9403 (t0) cc_final: 0.8895 (t0) REVERT: A 10 LYS cc_start: 0.9291 (ptpp) cc_final: 0.8868 (ptpp) REVERT: A 18 ASP cc_start: 0.9104 (m-30) cc_final: 0.8468 (p0) REVERT: C 44 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8858 (mm) REVERT: C 45 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.8924 (mptt) REVERT: C 194 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8546 (tp40) REVERT: G 219 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8076 (ptp) REVERT: G 232 MET cc_start: 0.7880 (tpp) cc_final: 0.7644 (tpp) REVERT: G 417 ASP cc_start: 0.9235 (OUTLIER) cc_final: 0.8870 (t70) REVERT: G 476 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8454 (mm-30) REVERT: H 391 MET cc_start: 0.8579 (tpp) cc_final: 0.7591 (tpt) outliers start: 24 outliers final: 14 residues processed: 83 average time/residue: 0.0806 time to fit residues: 10.5728 Evaluate side-chains 79 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 549 LEU Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 919 ILE Chi-restraints excluded: chain H residue 930 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 140 optimal weight: 0.5980 chunk 117 optimal weight: 0.0470 chunk 99 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN H 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.043587 restraints weight = 52803.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.045211 restraints weight = 28664.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.046299 restraints weight = 19738.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.047030 restraints weight = 15515.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.047505 restraints weight = 13199.889| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12205 Z= 0.098 Angle : 0.497 8.456 16477 Z= 0.261 Chirality : 0.042 0.150 1777 Planarity : 0.003 0.042 2130 Dihedral : 4.246 20.963 1571 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.33 % Rotamer: Outliers : 1.60 % Allowed : 17.44 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.85 (0.23), residues: 1423 helix: 1.79 (0.26), residues: 451 sheet: 0.95 (0.33), residues: 258 loop : -0.35 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 212 TYR 0.011 0.001 TYR G 223 PHE 0.012 0.001 PHE H 18 TRP 0.007 0.001 TRP D 144 HIS 0.003 0.000 HIS G 488 Details of bonding type rmsd covalent geometry : bond 0.00219 (12204) covalent geometry : angle 0.49595 (16475) SS BOND : bond 0.00017 ( 1) SS BOND : angle 2.70205 ( 2) hydrogen bonds : bond 0.03719 ( 456) hydrogen bonds : angle 3.91149 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.9402 (t0) cc_final: 0.9084 (t0) REVERT: A 18 ASP cc_start: 0.9124 (m-30) cc_final: 0.8470 (p0) REVERT: C 44 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8830 (mm) REVERT: C 45 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.8926 (mptt) REVERT: C 78 MET cc_start: 0.9290 (tpp) cc_final: 0.8947 (tpp) REVERT: C 194 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8554 (tp40) REVERT: G 219 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8222 (ptp) REVERT: G 232 MET cc_start: 0.7874 (tpp) cc_final: 0.7642 (tpp) REVERT: G 411 MET cc_start: 0.9301 (mmm) cc_final: 0.8926 (mmm) REVERT: G 417 ASP cc_start: 0.9241 (OUTLIER) cc_final: 0.8880 (t70) REVERT: G 476 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8450 (mm-30) REVERT: H 391 MET cc_start: 0.8496 (tpp) cc_final: 0.7610 (tpt) outliers start: 21 outliers final: 15 residues processed: 78 average time/residue: 0.0858 time to fit residues: 10.3664 Evaluate side-chains 79 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 549 LEU Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 581 ILE Chi-restraints excluded: chain H residue 919 ILE Chi-restraints excluded: chain H residue 930 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 90 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 113 optimal weight: 0.0030 chunk 107 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.059387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.043145 restraints weight = 53791.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.044766 restraints weight = 29227.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.045860 restraints weight = 20118.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.046588 restraints weight = 15817.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.047063 restraints weight = 13480.182| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12205 Z= 0.113 Angle : 0.505 8.520 16477 Z= 0.266 Chirality : 0.042 0.144 1777 Planarity : 0.003 0.042 2130 Dihedral : 4.283 20.358 1571 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 1.68 % Allowed : 17.29 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.70 (0.23), residues: 1423 helix: 1.52 (0.26), residues: 468 sheet: 0.97 (0.33), residues: 260 loop : -0.44 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 212 TYR 0.008 0.001 TYR H 19 PHE 0.012 0.001 PHE H 18 TRP 0.008 0.001 TRP D 144 HIS 0.003 0.001 HIS G 488 Details of bonding type rmsd covalent geometry : bond 0.00255 (12204) covalent geometry : angle 0.50426 (16475) SS BOND : bond 0.00033 ( 1) SS BOND : angle 2.69559 ( 2) hydrogen bonds : bond 0.03838 ( 456) hydrogen bonds : angle 3.94111 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.9403 (t0) cc_final: 0.9093 (t0) REVERT: A 18 ASP cc_start: 0.9149 (m-30) cc_final: 0.8454 (p0) REVERT: C 44 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8828 (mm) REVERT: C 45 LYS cc_start: 0.9481 (OUTLIER) cc_final: 0.8936 (mptt) REVERT: C 78 MET cc_start: 0.9321 (tpp) cc_final: 0.9010 (tpp) REVERT: C 194 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8569 (tp40) REVERT: G 219 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8203 (ptp) REVERT: G 232 MET cc_start: 0.7887 (tpp) cc_final: 0.7651 (tpp) REVERT: G 411 MET cc_start: 0.9292 (mmm) cc_final: 0.9008 (mmm) REVERT: G 417 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8936 (t70) REVERT: G 476 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8470 (mm-30) REVERT: H 391 MET cc_start: 0.8526 (tpp) cc_final: 0.7697 (tpt) outliers start: 22 outliers final: 15 residues processed: 79 average time/residue: 0.0953 time to fit residues: 11.3604 Evaluate side-chains 78 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain G residue 219 MET Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 549 LEU Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain H residue 919 ILE Chi-restraints excluded: chain H residue 930 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 10 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 139 optimal weight: 0.0870 chunk 126 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3165 r_free = 0.3165 target = 0.060389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.044198 restraints weight = 53082.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.045846 restraints weight = 28700.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.046953 restraints weight = 19732.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.047702 restraints weight = 15457.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.048192 restraints weight = 13129.139| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12205 Z= 0.091 Angle : 0.491 8.488 16477 Z= 0.257 Chirality : 0.042 0.133 1777 Planarity : 0.003 0.043 2130 Dihedral : 4.091 19.578 1571 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.25 % Favored : 97.68 % Rotamer: Outliers : 1.68 % Allowed : 17.67 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.94 (0.23), residues: 1423 helix: 1.85 (0.26), residues: 453 sheet: 1.03 (0.33), residues: 262 loop : -0.32 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 212 TYR 0.011 0.001 TYR G 223 PHE 0.012 0.001 PHE H 18 TRP 0.007 0.001 TRP H 477 HIS 0.003 0.000 HIS G 488 Details of bonding type rmsd covalent geometry : bond 0.00201 (12204) covalent geometry : angle 0.48975 (16475) SS BOND : bond 0.00043 ( 1) SS BOND : angle 2.59165 ( 2) hydrogen bonds : bond 0.03367 ( 456) hydrogen bonds : angle 3.78025 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1621.98 seconds wall clock time: 28 minutes 45.62 seconds (1725.62 seconds total)