Starting phenix.real_space_refine on Thu Mar 5 04:49:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z6f_11092/03_2026/6z6f_11092.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z6f_11092/03_2026/6z6f_11092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6z6f_11092/03_2026/6z6f_11092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z6f_11092/03_2026/6z6f_11092.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z6f_11092/03_2026/6z6f_11092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z6f_11092/03_2026/6z6f_11092.map" } resolution = 3.11 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= 0.020 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 88 5.16 5 C 12208 2.51 5 N 3255 2.21 5 O 3664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19217 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5178 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 615} Chain breaks: 2 Chain: "B" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5245 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4376 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain breaks: 3 Chain: "C" Number of atoms: 4416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4416 Classifications: {'peptide': 541} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 520} Chain breaks: 6 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.57, per 1000 atoms: 0.19 Number of scatterers: 19217 At special positions: 0 Unit cell: (126.367, 142.901, 218.485, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 88 16.00 O 3664 8.00 N 3255 7.00 C 12208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 359 " - pdb=" SG CYS C 366 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 702.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 247 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" ND1 HIS B 247 " 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 52.6% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.863A pdb=" N ASP A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.542A pdb=" N ILE A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 147 removed outlier: 3.810A pdb=" N GLU A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 171 through 190 Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 220 through 232 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 289 through 293 removed outlier: 3.773A pdb=" N GLY A 292 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 removed outlier: 3.811A pdb=" N TYR A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.590A pdb=" N MET A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.935A pdb=" N TYR A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 356 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 396 removed outlier: 3.505A pdb=" N GLY A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 428 removed outlier: 3.887A pdb=" N ILE A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 474 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.881A pdb=" N GLU A 498 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 499 " --> pdb=" O ILE A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 499' Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 562 through 580 removed outlier: 3.501A pdb=" N TYR A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 584 removed outlier: 3.590A pdb=" N PHE A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 636 through 645 Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 679 through 699 removed outlier: 5.861A pdb=" N GLU A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 87 through 100 removed outlier: 4.173A pdb=" N TYR B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 removed outlier: 3.673A pdb=" N ILE B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.533A pdb=" N LEU B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.777A pdb=" N GLY B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 191 Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.975A pdb=" N PHE B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 274 removed outlier: 3.891A pdb=" N LYS B 274 " --> pdb=" O GLU B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 274' Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.727A pdb=" N TYR B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 327 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.826A pdb=" N TYR B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 356 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 396 Processing helix chain 'B' and resid 410 through 428 removed outlier: 3.509A pdb=" N ILE B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 474 Processing helix chain 'B' and resid 486 through 489 removed outlier: 3.773A pdb=" N THR B 489 " --> pdb=" O PRO B 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 486 through 489' Processing helix chain 'B' and resid 495 through 499 removed outlier: 3.510A pdb=" N SER B 499 " --> pdb=" O ILE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 534 No H-bonds generated for 'chain 'B' and resid 532 through 534' Processing helix chain 'B' and resid 535 through 544 removed outlier: 3.799A pdb=" N ASP B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 544 " --> pdb=" O TRP B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 579 Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'B' and resid 599 through 607 removed outlier: 3.539A pdb=" N LEU B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 4.335A pdb=" N GLU B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 687 through 700 Processing helix chain 'D' and resid 38 through 52 removed outlier: 3.792A pdb=" N HIS D 52 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 61 Processing helix chain 'D' and resid 70 through 87 removed outlier: 3.762A pdb=" N MET D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.861A pdb=" N TYR D 95 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.994A pdb=" N ASN D 112 " --> pdb=" O HIS D 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 124 Processing helix chain 'D' and resid 140 through 151 removed outlier: 3.689A pdb=" N ASP D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 214 through 221 Processing helix chain 'D' and resid 243 through 252 Processing helix chain 'D' and resid 259 through 275 removed outlier: 3.627A pdb=" N LEU D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 295 through 301 Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.514A pdb=" N VAL D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 328 " --> pdb=" O ARG D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 443 removed outlier: 4.092A pdb=" N SER D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 515 Processing helix chain 'D' and resid 522 through 633 removed outlier: 4.542A pdb=" N ASN D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 639 removed outlier: 3.898A pdb=" N GLN D 639 " --> pdb=" O ARG D 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 42 removed outlier: 5.652A pdb=" N LYS C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 37 " --> pdb=" O HIS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 86 Processing helix chain 'C' and resid 87 through 92 removed outlier: 4.022A pdb=" N VAL C 92 " --> pdb=" O SER C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 104 removed outlier: 3.526A pdb=" N ARG C 102 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU C 104 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 111 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.682A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 243 through 249 removed outlier: 3.565A pdb=" N ASP C 249 " --> pdb=" O HIS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 282 removed outlier: 4.268A pdb=" N LEU C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 326 through 341 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 413 through 437 Processing helix chain 'C' and resid 439 through 511 removed outlier: 3.970A pdb=" N LEU C 443 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS C 476 " --> pdb=" O GLN C 472 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN C 511 " --> pdb=" O GLN C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 601 removed outlier: 3.936A pdb=" N SER C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 601 " --> pdb=" O ASN C 597 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.630A pdb=" N LEU A 374 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 331 " --> pdb=" O CYS A 371 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 373 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE A 333 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N MET A 240 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N SER A 334 " --> pdb=" O MET A 240 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 242 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 239 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL A 265 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE A 241 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU A 267 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP A 243 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N ARG A 269 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.168A pdb=" N ILE A 503 " --> pdb=" O ILE A 549 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL A 551 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 505 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE A 590 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR A 617 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N LEU A 647 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 618 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N PHE A 649 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN A 620 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 511 through 516 removed outlier: 3.634A pdb=" N ASP A 511 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS A 515 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER A 527 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 121 removed outlier: 6.104A pdb=" N THR B 58 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE B 121 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 60 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY B 59 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 239 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL B 265 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE B 241 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU B 267 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 243 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ARG B 269 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 476 through 478 removed outlier: 4.697A pdb=" N VAL B 490 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 503 " --> pdb=" O ILE B 549 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL B 551 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 505 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 502 " --> pdb=" O ALA B 591 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE B 593 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 504 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE B 595 " --> pdb=" O ILE B 504 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B 506 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ILE B 619 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE B 592 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE B 621 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY B 594 " --> pdb=" O PHE B 621 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 618 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE B 649 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN B 620 " --> pdb=" O PHE B 649 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU B 673 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 648 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 513 Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 35 removed outlier: 3.504A pdb=" N ARG D 237 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 239 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 35 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 203 " --> pdb=" O ALA D 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 16 removed outlier: 3.716A pdb=" N LEU C 291 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS C 140 " --> pdb=" O MET C 260 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ILE C 262 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C 142 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS C 141 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ALA C 241 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE C 143 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG C 164 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU C 240 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS C 166 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N THR C 242 " --> pdb=" O LYS C 166 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2721 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: 2.53 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5587 1.34 - 1.46: 3846 1.46 - 1.58: 10033 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 19602 Sorted by residual: bond pdb=" CG LEU A 573 " pdb=" CD2 LEU A 573 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.11e+00 bond pdb=" C VAL D 105 " pdb=" N PRO D 106 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.36e-02 5.41e+03 4.57e+00 bond pdb=" CB VAL A 200 " pdb=" CG1 VAL A 200 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.25e+00 bond pdb=" C GLU B 559 " pdb=" N PRO B 560 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.80e+00 bond pdb=" C VAL C 441 " pdb=" N PRO C 442 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.72e+00 ... (remaining 19597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 25646 2.50 - 5.00: 713 5.00 - 7.50: 118 7.50 - 10.01: 19 10.01 - 12.51: 4 Bond angle restraints: 26500 Sorted by residual: angle pdb=" C PRO A 456 " pdb=" N LEU A 457 " pdb=" CA LEU A 457 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C LEU B 555 " pdb=" N THR B 556 " pdb=" CA THR B 556 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" CA THR B 493 " pdb=" CB THR B 493 " pdb=" CG2 THR B 493 " ideal model delta sigma weight residual 110.50 117.83 -7.33 1.70e+00 3.46e-01 1.86e+01 angle pdb=" CA GLU C 350 " pdb=" CB GLU C 350 " pdb=" CG GLU C 350 " ideal model delta sigma weight residual 114.10 122.47 -8.37 2.00e+00 2.50e-01 1.75e+01 angle pdb=" N ILE B 450 " pdb=" CA ILE B 450 " pdb=" C ILE B 450 " ideal model delta sigma weight residual 112.29 108.37 3.92 9.40e-01 1.13e+00 1.74e+01 ... (remaining 26495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 10512 18.04 - 36.08: 1088 36.08 - 54.12: 281 54.12 - 72.16: 46 72.16 - 90.19: 33 Dihedral angle restraints: 11960 sinusoidal: 4947 harmonic: 7013 Sorted by residual: dihedral pdb=" CA SER B 54 " pdb=" C SER B 54 " pdb=" N PRO B 55 " pdb=" CA PRO B 55 " ideal model delta harmonic sigma weight residual 180.00 135.87 44.13 0 5.00e+00 4.00e-02 7.79e+01 dihedral pdb=" CA SER A 54 " pdb=" C SER A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta harmonic sigma weight residual 180.00 137.35 42.65 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CA LEU B 32 " pdb=" C LEU B 32 " pdb=" N SER B 33 " pdb=" CA SER B 33 " ideal model delta harmonic sigma weight residual 180.00 145.70 34.30 0 5.00e+00 4.00e-02 4.71e+01 ... (remaining 11957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2403 0.072 - 0.145: 477 0.145 - 0.217: 70 0.217 - 0.290: 8 0.290 - 0.362: 3 Chirality restraints: 2961 Sorted by residual: chirality pdb=" CG LEU C 536 " pdb=" CB LEU C 536 " pdb=" CD1 LEU C 536 " pdb=" CD2 LEU C 536 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CB ILE B 530 " pdb=" CA ILE B 530 " pdb=" CG1 ILE B 530 " pdb=" CG2 ILE B 530 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA PHE C 512 " pdb=" N PHE C 512 " pdb=" C PHE C 512 " pdb=" CB PHE C 512 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 2958 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 457 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C LEU A 457 " -0.073 2.00e-02 2.50e+03 pdb=" O LEU A 457 " 0.027 2.00e-02 2.50e+03 pdb=" N GLN A 458 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 54 " 0.060 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO B 55 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 54 " -0.057 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO A 55 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " -0.048 5.00e-02 4.00e+02 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 657 2.71 - 3.26: 18654 3.26 - 3.80: 28959 3.80 - 4.35: 35765 4.35 - 4.90: 61035 Nonbonded interactions: 145070 Sorted by model distance: nonbonded pdb=" OD2 ASP A 338 " pdb="ZN ZN A 801 " model vdw 2.160 2.230 nonbonded pdb=" O GLU D 565 " pdb=" OG1 THR D 568 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR A 468 " pdb=" OD2 ASP A 532 " model vdw 2.229 3.040 nonbonded pdb=" OD2 ASP B 338 " pdb="ZN ZN B 801 " model vdw 2.248 2.230 nonbonded pdb=" O VAL B 481 " pdb=" OH TYR B 575 " model vdw 2.262 3.040 ... (remaining 145065 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 'A' and (resid 40 through 515 or (resid 516 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 517 through 656 or resid 667 through 678 or resid 680 through 801)) selection = (chain 'B' and (resid 40 through 439 or resid 445 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.94 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 16.150 Find NCS groups from input model: 0.190 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.006 0.082 19605 Z= 0.293 Angle : 1.018 12.508 26502 Z= 0.572 Chirality : 0.060 0.362 2961 Planarity : 0.007 0.090 3405 Dihedral : 16.346 90.195 7413 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.14 % Favored : 92.82 % Rotamer: Outliers : 3.55 % Allowed : 19.18 % Favored : 77.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % Twisted General : 0.09 % 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: -2.88 (0.15), residues: 2353 helix: -0.42 (0.14), residues: 1164 sheet: -2.09 (0.31), residues: 228 loop : -3.86 (0.16), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 462 TYR 0.039 0.003 TYR A 468 PHE 0.029 0.002 PHE A 643 TRP 0.024 0.002 TRP C 391 HIS 0.020 0.002 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00604 (19602) covalent geometry : angle 1.01752 (26500) SS BOND : bond 0.00273 ( 1) SS BOND : angle 1.29500 ( 2) hydrogen bonds : bond 0.15119 ( 930) hydrogen bonds : angle 5.38194 ( 2721) metal coordination : bond 0.05415 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 162 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.8637 (t80) REVERT: A 404 ASP cc_start: 0.8751 (t0) cc_final: 0.8543 (t0) REVERT: B 289 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 374 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8847 (tt) REVERT: B 416 MET cc_start: 0.8513 (tmm) cc_final: 0.8302 (tmm) REVERT: B 566 MET cc_start: 0.8731 (tpp) cc_final: 0.8402 (tpp) REVERT: B 599 TYR cc_start: 0.8130 (t80) cc_final: 0.7916 (t80) REVERT: D 201 MET cc_start: 0.8286 (ptm) cc_final: 0.7861 (ppp) REVERT: D 327 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9051 (mm) REVERT: D 419 HIS cc_start: 0.7171 (t-90) cc_final: 0.6920 (t-90) REVERT: D 425 MET cc_start: 0.7881 (mmt) cc_final: 0.7631 (mmt) REVERT: D 429 TYR cc_start: 0.8348 (t80) cc_final: 0.8051 (t80) REVERT: D 455 PHE cc_start: 0.8741 (m-10) cc_final: 0.8528 (m-80) REVERT: C 155 GLU cc_start: 0.8761 (tt0) cc_final: 0.8522 (tt0) REVERT: C 552 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: C 630 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6752 (mtmm) outliers start: 77 outliers final: 41 residues processed: 239 average time/residue: 0.1393 time to fit residues: 50.1735 Evaluate side-chains 156 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 630 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 167 ASN A 268 HIS A 286 GLN A 379 ASN A 465 GLN A 651 ASN ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 500 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN B 682 ASN D 156 HIS D 419 HIS D 479 ASN D 512 GLN D 564 ASN C 87 HIS C 308 ASN C 497 ASN C 623 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.080183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.060710 restraints weight = 58558.993| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.19 r_work: 0.3021 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19605 Z= 0.138 Angle : 0.590 7.973 26502 Z= 0.311 Chirality : 0.042 0.159 2961 Planarity : 0.004 0.079 3405 Dihedral : 6.911 67.977 2649 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.15 % Allowed : 19.78 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: -1.25 (0.17), residues: 2353 helix: 1.01 (0.15), residues: 1130 sheet: -1.27 (0.32), residues: 238 loop : -3.06 (0.17), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 98 TYR 0.035 0.001 TYR D 410 PHE 0.020 0.001 PHE D 586 TRP 0.009 0.001 TRP D 298 HIS 0.008 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00291 (19602) covalent geometry : angle 0.58993 (26500) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.35249 ( 2) hydrogen bonds : bond 0.05949 ( 930) hydrogen bonds : angle 4.30419 ( 2721) metal coordination : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 127 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9545 (OUTLIER) cc_final: 0.8896 (t80) REVERT: A 404 ASP cc_start: 0.9147 (t0) cc_final: 0.8757 (t0) REVERT: B 289 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8522 (tm-30) REVERT: B 480 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7715 (pp) REVERT: B 599 TYR cc_start: 0.8204 (t80) cc_final: 0.7994 (t80) REVERT: D 201 MET cc_start: 0.8283 (ptm) cc_final: 0.7835 (ppp) REVERT: D 327 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9132 (mm) REVERT: D 425 MET cc_start: 0.8077 (mmt) cc_final: 0.7789 (mmt) REVERT: D 433 CYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8064 (p) REVERT: D 455 PHE cc_start: 0.8675 (m-10) cc_final: 0.8443 (m-80) REVERT: D 543 ARG cc_start: 0.9392 (tpt170) cc_final: 0.9044 (mtm110) REVERT: C 81 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8296 (tp) REVERT: C 484 ARG cc_start: 0.8287 (mmp80) cc_final: 0.8008 (mmp80) REVERT: C 495 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9199 (mm) REVERT: C 515 LEU cc_start: 0.8437 (pt) cc_final: 0.8230 (tp) REVERT: C 630 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6761 (mtmm) outliers start: 90 outliers final: 47 residues processed: 208 average time/residue: 0.1198 time to fit residues: 40.1835 Evaluate side-chains 169 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 115 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 ASN Chi-restraints excluded: chain C residue 630 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 49 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS A 360 HIS A 507 HIS ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS B 206 HIS B 268 HIS D 316 GLN ** D 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN C 555 GLN C 589 GLN C 623 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.077635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.057355 restraints weight = 60787.112| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.25 r_work: 0.2949 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19605 Z= 0.252 Angle : 0.655 8.564 26502 Z= 0.343 Chirality : 0.045 0.152 2961 Planarity : 0.005 0.082 3405 Dihedral : 6.038 56.219 2599 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.89 % Allowed : 20.06 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % Twisted General : 0.04 % 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: -0.77 (0.17), residues: 2353 helix: 1.39 (0.15), residues: 1168 sheet: -0.99 (0.33), residues: 235 loop : -2.99 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 628 TYR 0.040 0.002 TYR D 549 PHE 0.014 0.001 PHE D 602 TRP 0.009 0.001 TRP B 313 HIS 0.008 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00579 (19602) covalent geometry : angle 0.65510 (26500) SS BOND : bond 0.00243 ( 1) SS BOND : angle 0.99788 ( 2) hydrogen bonds : bond 0.06747 ( 930) hydrogen bonds : angle 4.46208 ( 2721) metal coordination : bond 0.00187 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 119 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9586 (OUTLIER) cc_final: 0.8834 (t80) REVERT: A 404 ASP cc_start: 0.9208 (t0) cc_final: 0.8813 (t0) REVERT: B 149 MET cc_start: 0.8677 (mtt) cc_final: 0.8458 (mtt) REVERT: B 480 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7946 (pp) REVERT: B 566 MET cc_start: 0.8993 (mmt) cc_final: 0.8679 (tpp) REVERT: B 599 TYR cc_start: 0.8442 (t80) cc_final: 0.8003 (t80) REVERT: D 96 MET cc_start: 0.8488 (mtp) cc_final: 0.8250 (tpp) REVERT: D 327 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9126 (mm) REVERT: D 425 MET cc_start: 0.8181 (mmt) cc_final: 0.7894 (mmt) REVERT: D 455 PHE cc_start: 0.8649 (m-10) cc_final: 0.8355 (m-80) REVERT: D 625 MET cc_start: 0.8590 (mmm) cc_final: 0.8332 (tpt) REVERT: C 495 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9216 (mm) REVERT: C 515 LEU cc_start: 0.8365 (pt) cc_final: 0.8156 (tp) REVERT: C 557 ASN cc_start: 0.8736 (t0) cc_final: 0.8502 (t0) outliers start: 106 outliers final: 75 residues processed: 220 average time/residue: 0.1141 time to fit residues: 40.3135 Evaluate side-chains 187 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 108 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 ASN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 584 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 45 optimal weight: 0.1980 chunk 164 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 186 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 HIS D 488 ASN C 623 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.080617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060649 restraints weight = 58681.631| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.26 r_work: 0.2996 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19605 Z= 0.118 Angle : 0.554 8.001 26502 Z= 0.287 Chirality : 0.041 0.159 2961 Planarity : 0.004 0.074 3405 Dihedral : 5.395 53.937 2592 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.41 % Allowed : 21.62 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: -0.13 (0.18), residues: 2353 helix: 1.90 (0.15), residues: 1176 sheet: -0.67 (0.33), residues: 240 loop : -2.69 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 666 TYR 0.028 0.001 TYR D 410 PHE 0.016 0.001 PHE D 586 TRP 0.010 0.001 TRP B 301 HIS 0.005 0.001 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00237 (19602) covalent geometry : angle 0.55372 (26500) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.28640 ( 2) hydrogen bonds : bond 0.05345 ( 930) hydrogen bonds : angle 4.03865 ( 2721) metal coordination : bond 0.00073 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 123 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9544 (OUTLIER) cc_final: 0.8860 (t80) REVERT: A 404 ASP cc_start: 0.9213 (t0) cc_final: 0.8769 (t0) REVERT: B 149 MET cc_start: 0.8508 (mtt) cc_final: 0.8230 (mtt) REVERT: B 566 MET cc_start: 0.9054 (mmt) cc_final: 0.8787 (tpp) REVERT: D 74 MET cc_start: 0.7888 (mmp) cc_final: 0.7485 (mmt) REVERT: D 96 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8269 (tpp) REVERT: D 201 MET cc_start: 0.8424 (ptm) cc_final: 0.7907 (ppp) REVERT: D 327 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9018 (mm) REVERT: D 425 MET cc_start: 0.7977 (mmt) cc_final: 0.7662 (mmt) REVERT: D 433 CYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8187 (p) REVERT: D 455 PHE cc_start: 0.8640 (m-10) cc_final: 0.8365 (m-80) REVERT: D 476 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.8999 (pt0) REVERT: D 625 MET cc_start: 0.8520 (mmm) cc_final: 0.8268 (tpt) REVERT: D 626 ASP cc_start: 0.8834 (t0) cc_final: 0.8283 (m-30) REVERT: C 229 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8544 (mmtm) REVERT: C 495 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9167 (mm) REVERT: C 513 ASN cc_start: 0.5718 (OUTLIER) cc_final: 0.5456 (p0) REVERT: C 515 LEU cc_start: 0.8369 (pt) cc_final: 0.7863 (tp) REVERT: C 585 LEU cc_start: 0.8030 (tp) cc_final: 0.7592 (tp) outliers start: 74 outliers final: 39 residues processed: 189 average time/residue: 0.1228 time to fit residues: 37.2370 Evaluate side-chains 160 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 532 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 102 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 226 optimal weight: 0.4980 chunk 173 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 96 optimal weight: 0.0870 chunk 152 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 194 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 517 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.080337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060352 restraints weight = 58683.603| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.26 r_work: 0.2981 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19605 Z= 0.123 Angle : 0.549 10.291 26502 Z= 0.282 Chirality : 0.041 0.161 2961 Planarity : 0.004 0.076 3405 Dihedral : 5.115 53.317 2589 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.55 % Allowed : 21.72 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: 0.16 (0.18), residues: 2353 helix: 2.11 (0.15), residues: 1181 sheet: -0.56 (0.34), residues: 245 loop : -2.53 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 666 TYR 0.024 0.001 TYR D 410 PHE 0.013 0.001 PHE D 602 TRP 0.007 0.001 TRP A 313 HIS 0.004 0.001 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00260 (19602) covalent geometry : angle 0.54901 (26500) SS BOND : bond 0.00218 ( 1) SS BOND : angle 0.49827 ( 2) hydrogen bonds : bond 0.05301 ( 930) hydrogen bonds : angle 3.96560 ( 2721) metal coordination : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 120 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9559 (OUTLIER) cc_final: 0.8806 (t80) REVERT: A 404 ASP cc_start: 0.9208 (t0) cc_final: 0.8758 (t0) REVERT: A 640 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8086 (tp30) REVERT: B 149 MET cc_start: 0.8413 (mtt) cc_final: 0.8126 (mtt) REVERT: B 566 MET cc_start: 0.8976 (mmt) cc_final: 0.8614 (tpp) REVERT: D 96 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8279 (tpp) REVERT: D 201 MET cc_start: 0.8382 (ptm) cc_final: 0.7799 (ppp) REVERT: D 327 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9062 (mm) REVERT: D 410 TYR cc_start: 0.7453 (m-80) cc_final: 0.7243 (m-80) REVERT: D 425 MET cc_start: 0.8024 (mmt) cc_final: 0.7686 (mmt) REVERT: D 433 CYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8159 (p) REVERT: D 455 PHE cc_start: 0.8655 (m-10) cc_final: 0.8394 (m-80) REVERT: D 476 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.8975 (pt0) REVERT: D 625 MET cc_start: 0.8478 (mmm) cc_final: 0.8210 (tpt) REVERT: D 626 ASP cc_start: 0.8885 (t0) cc_final: 0.8351 (m-30) REVERT: C 229 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8625 (mmtm) REVERT: C 458 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8445 (t0) REVERT: C 495 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9170 (mm) REVERT: C 515 LEU cc_start: 0.8402 (pt) cc_final: 0.8047 (tp) REVERT: C 589 GLN cc_start: 0.8440 (mt0) cc_final: 0.8116 (tp-100) outliers start: 77 outliers final: 46 residues processed: 189 average time/residue: 0.1259 time to fit residues: 38.2379 Evaluate side-chains 169 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 115 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 158 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.079448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059446 restraints weight = 58446.959| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.25 r_work: 0.2962 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19605 Z= 0.154 Angle : 0.571 10.692 26502 Z= 0.294 Chirality : 0.042 0.146 2961 Planarity : 0.004 0.075 3405 Dihedral : 5.140 52.519 2589 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.20 % Allowed : 21.30 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: 0.28 (0.18), residues: 2353 helix: 2.17 (0.15), residues: 1179 sheet: -0.38 (0.34), residues: 244 loop : -2.44 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 666 TYR 0.023 0.001 TYR D 410 PHE 0.019 0.001 PHE D 586 TRP 0.011 0.001 TRP D 298 HIS 0.007 0.001 HIS D 482 Details of bonding type rmsd covalent geometry : bond 0.00345 (19602) covalent geometry : angle 0.57060 (26500) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.70504 ( 2) hydrogen bonds : bond 0.05560 ( 930) hydrogen bonds : angle 4.01269 ( 2721) metal coordination : bond 0.00110 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 118 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9557 (OUTLIER) cc_final: 0.8808 (t80) REVERT: A 397 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: A 404 ASP cc_start: 0.9234 (t0) cc_final: 0.8758 (t0) REVERT: A 640 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: B 149 MET cc_start: 0.8343 (mtt) cc_final: 0.8016 (mtt) REVERT: B 480 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7781 (pp) REVERT: B 566 MET cc_start: 0.8897 (mmt) cc_final: 0.8559 (tpp) REVERT: D 327 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9047 (mm) REVERT: D 410 TYR cc_start: 0.7459 (m-80) cc_final: 0.7196 (m-80) REVERT: D 425 MET cc_start: 0.7998 (mmt) cc_final: 0.7683 (mmt) REVERT: D 455 PHE cc_start: 0.8689 (m-10) cc_final: 0.8423 (m-80) REVERT: D 625 MET cc_start: 0.8490 (mmm) cc_final: 0.8177 (tpt) REVERT: C 229 LYS cc_start: 0.8925 (mmtm) cc_final: 0.8631 (mmtm) REVERT: C 293 VAL cc_start: 0.5466 (OUTLIER) cc_final: 0.5183 (t) REVERT: C 422 MET cc_start: 0.9261 (ttm) cc_final: 0.8958 (ttm) REVERT: C 458 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8458 (t0) REVERT: C 495 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9145 (mm) REVERT: C 589 GLN cc_start: 0.8439 (mt0) cc_final: 0.8121 (tp-100) outliers start: 91 outliers final: 67 residues processed: 199 average time/residue: 0.1259 time to fit residues: 40.2085 Evaluate side-chains 189 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 114 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 112 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 236 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 202 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 158 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.081032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060915 restraints weight = 58570.051| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.29 r_work: 0.3005 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19605 Z= 0.114 Angle : 0.541 11.428 26502 Z= 0.276 Chirality : 0.041 0.150 2961 Planarity : 0.004 0.073 3405 Dihedral : 4.926 51.955 2589 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.32 % Allowed : 22.18 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2353 helix: 2.32 (0.15), residues: 1183 sheet: -0.37 (0.33), residues: 257 loop : -2.29 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 666 TYR 0.021 0.001 TYR D 410 PHE 0.013 0.001 PHE D 602 TRP 0.009 0.001 TRP B 301 HIS 0.004 0.001 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00239 (19602) covalent geometry : angle 0.54070 (26500) SS BOND : bond 0.00171 ( 1) SS BOND : angle 0.52441 ( 2) hydrogen bonds : bond 0.04984 ( 930) hydrogen bonds : angle 3.86895 ( 2721) metal coordination : bond 0.00073 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 124 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9543 (OUTLIER) cc_final: 0.8838 (t80) REVERT: A 397 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: A 404 ASP cc_start: 0.9220 (t0) cc_final: 0.8737 (t0) REVERT: A 640 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: B 66 MET cc_start: 0.9451 (mtm) cc_final: 0.9216 (mtp) REVERT: D 201 MET cc_start: 0.8383 (ptm) cc_final: 0.7597 (ppp) REVERT: D 327 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8885 (mm) REVERT: D 410 TYR cc_start: 0.7355 (m-80) cc_final: 0.7114 (m-80) REVERT: D 425 MET cc_start: 0.8020 (mmt) cc_final: 0.7619 (mmt) REVERT: D 433 CYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8097 (p) REVERT: D 455 PHE cc_start: 0.8649 (m-10) cc_final: 0.8397 (m-80) REVERT: C 94 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8448 (t-90) REVERT: C 229 LYS cc_start: 0.8912 (mmtm) cc_final: 0.8609 (mmtm) REVERT: C 256 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.6299 (m-80) REVERT: C 422 MET cc_start: 0.9265 (ttm) cc_final: 0.8982 (ttm) REVERT: C 458 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8434 (t0) REVERT: C 484 ARG cc_start: 0.8410 (mmp80) cc_final: 0.8107 (mmp80) REVERT: C 495 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9117 (mm) REVERT: C 589 GLN cc_start: 0.8460 (mt0) cc_final: 0.8106 (tp-100) REVERT: C 623 GLN cc_start: 0.7646 (tp40) cc_final: 0.7010 (pp30) REVERT: C 628 ARG cc_start: 0.9153 (ttt-90) cc_final: 0.8948 (ttt90) outliers start: 72 outliers final: 49 residues processed: 188 average time/residue: 0.1097 time to fit residues: 33.8630 Evaluate side-chains 173 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 115 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 256 TYR Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 221 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 117 optimal weight: 0.1980 chunk 161 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.061290 restraints weight = 58863.900| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.29 r_work: 0.3014 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19605 Z= 0.112 Angle : 0.548 11.863 26502 Z= 0.277 Chirality : 0.041 0.144 2961 Planarity : 0.004 0.072 3405 Dihedral : 4.754 51.862 2587 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.00 % Allowed : 22.36 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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 (0.19), residues: 2353 helix: 2.43 (0.15), residues: 1187 sheet: -0.24 (0.34), residues: 257 loop : -2.15 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 666 TYR 0.021 0.001 TYR A 468 PHE 0.024 0.001 PHE D 586 TRP 0.007 0.001 TRP B 313 HIS 0.004 0.000 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00235 (19602) covalent geometry : angle 0.54805 (26500) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.58458 ( 2) hydrogen bonds : bond 0.04846 ( 930) hydrogen bonds : angle 3.80666 ( 2721) metal coordination : bond 0.00055 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 122 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9540 (OUTLIER) cc_final: 0.8822 (t80) REVERT: A 397 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: A 404 ASP cc_start: 0.9195 (t0) cc_final: 0.8713 (t0) REVERT: A 640 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8252 (tp30) REVERT: B 289 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8900 (tm-30) REVERT: B 566 MET cc_start: 0.8324 (tpp) cc_final: 0.8017 (tpp) REVERT: D 201 MET cc_start: 0.8380 (ptm) cc_final: 0.7986 (ppp) REVERT: D 327 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9062 (mm) REVERT: D 410 TYR cc_start: 0.7336 (m-80) cc_final: 0.7067 (m-80) REVERT: D 425 MET cc_start: 0.7939 (mmt) cc_final: 0.7555 (mmt) REVERT: D 433 CYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8081 (p) REVERT: D 455 PHE cc_start: 0.8640 (m-10) cc_final: 0.8396 (m-80) REVERT: D 476 GLU cc_start: 0.9400 (OUTLIER) cc_final: 0.9091 (pt0) REVERT: C 179 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8414 (mmmt) REVERT: C 256 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.6117 (m-80) REVERT: C 422 MET cc_start: 0.9267 (ttm) cc_final: 0.8992 (ttm) REVERT: C 495 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9103 (mm) REVERT: C 589 GLN cc_start: 0.8472 (mt0) cc_final: 0.8104 (tp-100) outliers start: 65 outliers final: 49 residues processed: 181 average time/residue: 0.1190 time to fit residues: 34.9596 Evaluate side-chains 174 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 117 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 256 TYR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 184 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 chunk 94 optimal weight: 0.2980 chunk 159 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.080662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060565 restraints weight = 58620.098| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.27 r_work: 0.2993 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19605 Z= 0.133 Angle : 0.565 11.564 26502 Z= 0.287 Chirality : 0.041 0.146 2961 Planarity : 0.004 0.073 3405 Dihedral : 4.693 51.661 2583 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.04 % Allowed : 22.54 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: 0.71 (0.18), residues: 2353 helix: 2.44 (0.15), residues: 1183 sheet: -0.22 (0.34), residues: 257 loop : -2.15 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 628 TYR 0.022 0.001 TYR A 468 PHE 0.014 0.001 PHE D 602 TRP 0.008 0.001 TRP D 298 HIS 0.006 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00293 (19602) covalent geometry : angle 0.56495 (26500) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.70140 ( 2) hydrogen bonds : bond 0.05034 ( 930) hydrogen bonds : angle 3.84133 ( 2721) metal coordination : bond 0.00092 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 118 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9550 (OUTLIER) cc_final: 0.8836 (t80) REVERT: A 397 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: A 404 ASP cc_start: 0.9194 (t0) cc_final: 0.8709 (t0) REVERT: A 640 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8289 (tp30) REVERT: B 289 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8824 (tm-30) REVERT: B 566 MET cc_start: 0.8195 (tpp) cc_final: 0.7891 (tpp) REVERT: D 201 MET cc_start: 0.8398 (ptm) cc_final: 0.8021 (ppp) REVERT: D 327 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9068 (mm) REVERT: D 410 TYR cc_start: 0.7325 (m-80) cc_final: 0.7059 (m-80) REVERT: D 425 MET cc_start: 0.7970 (mmt) cc_final: 0.7597 (mmt) REVERT: D 433 CYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8136 (p) REVERT: D 455 PHE cc_start: 0.8678 (m-10) cc_final: 0.8440 (m-80) REVERT: D 476 GLU cc_start: 0.9401 (OUTLIER) cc_final: 0.9090 (pt0) REVERT: C 256 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.6230 (m-80) REVERT: C 422 MET cc_start: 0.9244 (ttm) cc_final: 0.9005 (ttm) REVERT: C 484 ARG cc_start: 0.8439 (mmp80) cc_final: 0.8133 (mmp80) REVERT: C 495 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9101 (mm) REVERT: C 589 GLN cc_start: 0.8437 (mt0) cc_final: 0.8179 (tp-100) REVERT: C 623 GLN cc_start: 0.7711 (tp40) cc_final: 0.7056 (pp30) outliers start: 66 outliers final: 53 residues processed: 179 average time/residue: 0.1227 time to fit residues: 35.8741 Evaluate side-chains 179 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 118 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 256 TYR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 228 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 0.0370 chunk 56 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 148 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.081016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060859 restraints weight = 58716.288| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.27 r_work: 0.3001 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19605 Z= 0.124 Angle : 0.575 12.484 26502 Z= 0.289 Chirality : 0.041 0.214 2961 Planarity : 0.004 0.072 3405 Dihedral : 4.594 51.935 2582 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.86 % Allowed : 22.54 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: 0.75 (0.18), residues: 2353 helix: 2.47 (0.15), residues: 1182 sheet: -0.19 (0.34), residues: 257 loop : -2.11 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 628 TYR 0.021 0.001 TYR A 468 PHE 0.027 0.001 PHE D 586 TRP 0.007 0.001 TRP D 298 HIS 0.005 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00271 (19602) covalent geometry : angle 0.57473 (26500) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.65269 ( 2) hydrogen bonds : bond 0.04938 ( 930) hydrogen bonds : angle 3.81471 ( 2721) metal coordination : bond 0.00072 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 122 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9547 (OUTLIER) cc_final: 0.8843 (t80) REVERT: A 397 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: A 404 ASP cc_start: 0.9194 (t0) cc_final: 0.8711 (t0) REVERT: A 640 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: B 289 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8825 (tm-30) REVERT: B 566 MET cc_start: 0.8232 (tpp) cc_final: 0.7923 (tpp) REVERT: D 201 MET cc_start: 0.8384 (ptm) cc_final: 0.7623 (ppp) REVERT: D 327 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9061 (mm) REVERT: D 410 TYR cc_start: 0.7324 (m-80) cc_final: 0.7039 (m-80) REVERT: D 425 MET cc_start: 0.7937 (mmt) cc_final: 0.7568 (mmt) REVERT: D 433 CYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8071 (p) REVERT: D 455 PHE cc_start: 0.8674 (m-10) cc_final: 0.8422 (m-80) REVERT: D 476 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.9099 (pt0) REVERT: C 256 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6236 (m-80) REVERT: C 422 MET cc_start: 0.9253 (ttm) cc_final: 0.9022 (ttm) REVERT: C 484 ARG cc_start: 0.8437 (mmp80) cc_final: 0.8135 (mmp80) REVERT: C 489 MET cc_start: 0.8965 (mmm) cc_final: 0.8756 (mmm) REVERT: C 495 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9118 (mm) REVERT: C 589 GLN cc_start: 0.8443 (mt0) cc_final: 0.8170 (tp-100) REVERT: C 623 GLN cc_start: 0.7530 (tp40) cc_final: 0.7024 (pp30) outliers start: 62 outliers final: 54 residues processed: 181 average time/residue: 0.1194 time to fit residues: 35.3129 Evaluate side-chains 181 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 119 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 256 TYR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 88 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 0.0980 chunk 182 optimal weight: 0.3980 chunk 162 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.081606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.061448 restraints weight = 58607.953| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.27 r_work: 0.3017 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19605 Z= 0.115 Angle : 0.563 11.980 26502 Z= 0.282 Chirality : 0.041 0.162 2961 Planarity : 0.004 0.072 3405 Dihedral : 4.531 52.038 2582 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.00 % Allowed : 22.41 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: 0.74 (0.18), residues: 2353 helix: 2.45 (0.15), residues: 1151 sheet: -0.16 (0.34), residues: 257 loop : -1.94 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 628 TYR 0.021 0.001 TYR D 410 PHE 0.014 0.001 PHE D 602 TRP 0.007 0.001 TRP A 313 HIS 0.007 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00247 (19602) covalent geometry : angle 0.56297 (26500) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.60405 ( 2) hydrogen bonds : bond 0.04749 ( 930) hydrogen bonds : angle 3.79249 ( 2721) metal coordination : bond 0.00085 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4651.02 seconds wall clock time: 82 minutes 9.35 seconds (4929.35 seconds total)