Starting phenix.real_space_refine on Thu Jul 2 19:41:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vwc_32152/07_2026/7vwc_32152.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vwc_32152/07_2026/7vwc_32152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vwc_32152/07_2026/7vwc_32152.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vwc_32152/07_2026/7vwc_32152.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vwc_32152/07_2026/7vwc_32152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vwc_32152/07_2026/7vwc_32152.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vwc_32152/07_2026/7vwc_32152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vwc_32152/07_2026/7vwc_32152.map" } resolution = 3.53 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= 0.006 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 P 2 5.49 5 S 46 5.16 5 C 6340 2.51 5 N 1741 2.21 5 O 1763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9892 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4929 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 21, 'TRANS': 595} Chain breaks: 2 Chain: "B" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4899 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'82T': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'82T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.10, per 1000 atoms: 0.21 Number of scatterers: 9892 At special positions: 0 Unit cell: (103.88, 147.34, 111.3, 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) S 46 16.00 P 2 15.00 O 1763 8.00 N 1741 7.00 C 6340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 274.3 milliseconds 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 7 sheets defined 61.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.698A pdb=" N LEU A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.753A pdb=" N VAL A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 124 removed outlier: 3.774A pdb=" N CYS A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.705A pdb=" N GLN A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN A 136 " --> pdb=" O TRP A 132 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 removed outlier: 3.981A pdb=" N VAL A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 175 removed outlier: 3.685A pdb=" N ARG A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 173 " --> pdb=" O HIS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 217 removed outlier: 3.604A pdb=" N PHE A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 235 removed outlier: 3.762A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 4.077A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.681A pdb=" N ARG A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.831A pdb=" N GLU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.811A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 344 through 354 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 374 through 380 removed outlier: 3.744A pdb=" N SER A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 407 through 430 removed outlier: 3.591A pdb=" N GLU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 removed outlier: 4.127A pdb=" N PHE A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.698A pdb=" N VAL A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 570 removed outlier: 3.912A pdb=" N GLN A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.771A pdb=" N ILE A 588 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 589 " --> pdb=" O HIS A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 585 through 589' Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 606 through 622 removed outlier: 3.684A pdb=" N LYS A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 612 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 649 removed outlier: 3.764A pdb=" N GLU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 645 " --> pdb=" O GLY A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 666 removed outlier: 3.845A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 666 " --> pdb=" O LEU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 700 removed outlier: 3.962A pdb=" N GLN A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.539A pdb=" N CYS A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.684A pdb=" N LEU B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 107 through 124 removed outlier: 3.555A pdb=" N VAL B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 removed outlier: 3.578A pdb=" N TRP B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.517A pdb=" N ALA B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 168 removed outlier: 3.554A pdb=" N GLY B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 removed outlier: 3.538A pdb=" N PHE B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 4.114A pdb=" N SER B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.734A pdb=" N ALA B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 234 removed outlier: 3.633A pdb=" N ASP B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 4.058A pdb=" N ILE B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 261 through 270 removed outlier: 3.771A pdb=" N PHE B 265 " --> pdb=" O PHE B 261 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.614A pdb=" N MET B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 removed outlier: 3.589A pdb=" N VAL B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.618A pdb=" N PHE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 312 removed outlier: 3.768A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 321 Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.864A pdb=" N PHE B 333 " --> pdb=" O MET B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 385 through 391 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 410 through 429 removed outlier: 4.233A pdb=" N GLY B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 514 through 521 removed outlier: 3.878A pdb=" N ARG B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.768A pdb=" N VAL B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 570 Processing helix chain 'B' and resid 575 through 583 removed outlier: 3.687A pdb=" N VAL B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 606 through 622 removed outlier: 3.721A pdb=" N GLY B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 619 " --> pdb=" O MET B 615 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS B 621 " --> pdb=" O ARG B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 651 removed outlier: 3.778A pdb=" N GLY B 641 " --> pdb=" O ILE B 637 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 643 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.652A pdb=" N LEU B 663 " --> pdb=" O ARG B 660 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TRP B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 660 through 664' Processing helix chain 'B' and resid 685 through 690 removed outlier: 3.506A pdb=" N LEU B 690 " --> pdb=" O SER B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 702 removed outlier: 3.919A pdb=" N ARG B 698 " --> pdb=" O GLU B 694 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 713 removed outlier: 3.631A pdb=" N MET B 709 " --> pdb=" O GLY B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 497 removed outlier: 3.652A pdb=" N VAL A 530 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 482 removed outlier: 6.860A pdb=" N ILE A 481 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 503 through 506 removed outlier: 6.790A pdb=" N LEU A 504 " --> pdb=" O LEU A 671 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 539 through 542 Processing sheet with id=AA5, first strand: chain 'B' and resid 467 through 469 removed outlier: 3.723A pdb=" N LYS B 533 " --> pdb=" O VAL B 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 505 through 506 removed outlier: 3.632A pdb=" N PHE B 673 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 539 through 542 removed outlier: 6.476A pdb=" N PHE B 540 " --> pdb=" O LEU B 627 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1578 1.31 - 1.43: 2725 1.43 - 1.56: 5711 1.56 - 1.69: 4 1.69 - 1.81: 76 Bond restraints: 10094 Sorted by residual: bond pdb=" C18 82T B 801 " pdb=" O20 82T B 801 " ideal model delta sigma weight residual 1.335 1.399 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C18 82T A 801 " pdb=" O20 82T A 801 " ideal model delta sigma weight residual 1.335 1.395 -0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" N TYR B 406 " pdb=" CA TYR B 406 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.31e-02 5.83e+03 5.14e+00 bond pdb=" N GLU A 380 " pdb=" CA GLU A 380 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.33e-02 5.65e+03 5.03e+00 bond pdb=" N THR B 693 " pdb=" CA THR B 693 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.35e-02 5.49e+03 4.37e+00 ... (remaining 10089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 13365 2.67 - 5.33: 240 5.33 - 8.00: 27 8.00 - 10.66: 8 10.66 - 13.33: 5 Bond angle restraints: 13645 Sorted by residual: angle pdb=" N TYR B 406 " pdb=" CA TYR B 406 " pdb=" C TYR B 406 " ideal model delta sigma weight residual 114.31 105.53 8.78 1.29e+00 6.01e-01 4.63e+01 angle pdb=" N ILE B 399 " pdb=" CA ILE B 399 " pdb=" C ILE B 399 " ideal model delta sigma weight residual 112.96 106.89 6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CA GLU A 471 " pdb=" C GLU A 471 " pdb=" O GLU A 471 " ideal model delta sigma weight residual 121.54 116.16 5.38 1.16e+00 7.43e-01 2.15e+01 angle pdb=" N THR B 693 " pdb=" CA THR B 693 " pdb=" C THR B 693 " ideal model delta sigma weight residual 113.43 107.67 5.76 1.26e+00 6.30e-01 2.09e+01 angle pdb=" O24 82T A 801 " pdb=" P25 82T A 801 " pdb=" O28 82T A 801 " ideal model delta sigma weight residual 97.38 110.71 -13.33 3.00e+00 1.11e-01 1.97e+01 ... (remaining 13640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.42: 5809 29.42 - 58.83: 239 58.83 - 88.25: 32 88.25 - 117.66: 2 117.66 - 147.08: 1 Dihedral angle restraints: 6083 sinusoidal: 2508 harmonic: 3575 Sorted by residual: dihedral pdb=" CA GLU A 682 " pdb=" C GLU A 682 " pdb=" N LYS A 683 " pdb=" CA LYS A 683 " ideal model delta harmonic sigma weight residual -180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU B 271 " pdb=" C GLU B 271 " pdb=" N GLU B 272 " pdb=" CA GLU B 272 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU B 690 " pdb=" C LEU B 690 " pdb=" N SER B 691 " pdb=" CA SER B 691 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 6080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 962 0.047 - 0.093: 453 0.093 - 0.140: 100 0.140 - 0.186: 5 0.186 - 0.233: 3 Chirality restraints: 1523 Sorted by residual: chirality pdb=" CA GLU A 471 " pdb=" N GLU A 471 " pdb=" C GLU A 471 " pdb=" CB GLU A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL B 347 " pdb=" CA VAL B 347 " pdb=" CG1 VAL B 347 " pdb=" CG2 VAL B 347 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE B 558 " pdb=" CA ILE B 558 " pdb=" CG1 ILE B 558 " pdb=" CG2 ILE B 558 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1520 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 236 " 0.030 2.00e-02 2.50e+03 6.28e-02 3.94e+01 pdb=" C ARG A 236 " -0.108 2.00e-02 2.50e+03 pdb=" O ARG A 236 " 0.042 2.00e-02 2.50e+03 pdb=" N GLY A 237 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 545 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.77e+00 pdb=" N PRO B 546 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 546 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 546 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 242 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 243 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.024 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 257 2.68 - 3.24: 9808 3.24 - 3.79: 14241 3.79 - 4.35: 20304 4.35 - 4.90: 32289 Nonbonded interactions: 76899 Sorted by model distance: nonbonded pdb=" O ASN B 318 " pdb=" ND2 ASN B 318 " model vdw 2.127 3.120 nonbonded pdb=" OG SER B 562 " pdb=" OD1 ASP B 565 " model vdw 2.218 3.040 nonbonded pdb=" NH2 ARG A 189 " pdb=" OD2 ASP A 428 " model vdw 2.230 3.120 nonbonded pdb=" NE2 GLN B 611 " pdb=" O CYS B 631 " model vdw 2.246 3.120 nonbonded pdb=" O GLU B 471 " pdb=" NZ LYS B 624 " model vdw 2.257 3.120 ... (remaining 76894 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 68 through 720 or resid 801)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.050 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.009 0.069 10094 Z= 0.372 Angle : 0.933 13.330 13645 Z= 0.502 Chirality : 0.052 0.233 1523 Planarity : 0.005 0.063 1728 Dihedral : 16.117 147.075 3779 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 0.38 % Allowed : 1.06 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.21), residues: 1217 helix: -3.47 (0.14), residues: 795 sheet: -2.35 (0.74), residues: 47 loop : -1.96 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 163 TYR 0.018 0.002 TYR B 174 PHE 0.018 0.002 PHE B 162 TRP 0.013 0.002 TRP A 326 HIS 0.006 0.002 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00858 / 0.37 (10094) covalent geometry : angle 0.93326 / 0.50 (13645) hydrogen bonds : bond 0.29371 / 19.70 ( 356) hydrogen bonds : angle 10.40196 / 7.25 ( 1020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7510 (mt-10) outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 0.0858 time to fit residues: 16.9639 Evaluate side-chains 121 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.0060 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109044 restraints weight = 13412.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107356 restraints weight = 11145.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108620 restraints weight = 10616.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109102 restraints weight = 8041.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109617 restraints weight = 7676.438| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10094 Z= 0.143 Angle : 0.675 9.907 13645 Z= 0.342 Chirality : 0.043 0.155 1523 Planarity : 0.004 0.060 1728 Dihedral : 8.545 122.988 1430 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.29 % Allowed : 7.98 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.22), residues: 1217 helix: -2.88 (0.16), residues: 789 sheet: -2.21 (0.69), residues: 57 loop : -1.86 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 285 TYR 0.012 0.001 TYR B 310 PHE 0.015 0.001 PHE A 673 TRP 0.011 0.001 TRP A 77 HIS 0.004 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10094) covalent geometry : angle 0.67472 / 0.34 (13645) hydrogen bonds : bond 0.05322 / 3.51 ( 356) hydrogen bonds : angle 6.05941 / 4.26 ( 1020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 411 GLU cc_start: 0.6702 (tt0) cc_final: 0.6411 (mt-10) REVERT: A 427 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 545 ARG cc_start: 0.7625 (ptt90) cc_final: 0.7405 (ptt-90) outliers start: 3 outliers final: 2 residues processed: 149 average time/residue: 0.0932 time to fit residues: 19.1798 Evaluate side-chains 129 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 68 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 GLN B 318 ASN B 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112521 restraints weight = 13251.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109994 restraints weight = 10738.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111299 restraints weight = 11793.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113012 restraints weight = 8149.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113147 restraints weight = 6853.332| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10094 Z= 0.105 Angle : 0.573 10.576 13645 Z= 0.289 Chirality : 0.040 0.201 1523 Planarity : 0.004 0.058 1728 Dihedral : 7.261 92.996 1430 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.29 % Allowed : 11.15 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.23), residues: 1217 helix: -2.33 (0.17), residues: 792 sheet: -2.13 (0.72), residues: 55 loop : -1.83 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 418 TYR 0.013 0.001 TYR A 620 PHE 0.013 0.001 PHE A 673 TRP 0.011 0.001 TRP A 601 HIS 0.004 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (10094) covalent geometry : angle 0.57338 / 0.29 (13645) hydrogen bonds : bond 0.03508 / 2.34 ( 356) hydrogen bonds : angle 5.05972 / 3.55 ( 1020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7089 (mt-10) REVERT: A 583 VAL cc_start: 0.8491 (t) cc_final: 0.8105 (m) REVERT: A 598 MET cc_start: 0.7263 (mtt) cc_final: 0.6984 (mtp) REVERT: A 615 MET cc_start: 0.7600 (mmm) cc_final: 0.7059 (tpp) REVERT: B 406 TYR cc_start: 0.6743 (t80) cc_final: 0.6248 (t80) REVERT: B 699 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6398 (tp) outliers start: 3 outliers final: 0 residues processed: 153 average time/residue: 0.0993 time to fit residues: 21.0729 Evaluate side-chains 127 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 699 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 98 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 115 optimal weight: 0.0670 overall best weight: 0.9526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN B 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.153914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111541 restraints weight = 13380.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110816 restraints weight = 10757.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112128 restraints weight = 9974.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112818 restraints weight = 7413.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113287 restraints weight = 6986.720| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10094 Z= 0.106 Angle : 0.553 10.033 13645 Z= 0.278 Chirality : 0.041 0.182 1523 Planarity : 0.003 0.053 1728 Dihedral : 6.551 71.707 1429 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.06 % Allowed : 13.85 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.23), residues: 1217 helix: -2.04 (0.17), residues: 791 sheet: -2.02 (0.73), residues: 55 loop : -1.78 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 660 TYR 0.015 0.001 TYR A 620 PHE 0.011 0.001 PHE A 673 TRP 0.007 0.001 TRP B 595 HIS 0.005 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (10094) covalent geometry : angle 0.55269 / 0.28 (13645) hydrogen bonds : bond 0.03227 / 2.16 ( 356) hydrogen bonds : angle 4.74095 / 3.32 ( 1020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6562 (ttt90) cc_final: 0.6113 (mmt90) REVERT: A 76 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7727 (tp) REVERT: A 427 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7026 (mt-10) REVERT: A 598 MET cc_start: 0.7272 (mtt) cc_final: 0.7002 (mtp) REVERT: B 567 GLN cc_start: 0.8021 (mt0) cc_final: 0.7651 (mm-40) REVERT: B 615 MET cc_start: 0.8483 (mmm) cc_final: 0.8113 (mmt) REVERT: B 622 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7375 (mtt-85) outliers start: 11 outliers final: 3 residues processed: 157 average time/residue: 0.0950 time to fit residues: 20.9911 Evaluate side-chains 134 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 98 optimal weight: 0.0070 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 502 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113731 restraints weight = 13207.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110393 restraints weight = 11610.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111461 restraints weight = 13846.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112975 restraints weight = 9438.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113286 restraints weight = 7722.704| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10094 Z= 0.108 Angle : 0.562 11.488 13645 Z= 0.279 Chirality : 0.041 0.192 1523 Planarity : 0.003 0.049 1728 Dihedral : 6.085 56.336 1429 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.06 % Allowed : 15.67 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.24), residues: 1217 helix: -1.88 (0.17), residues: 791 sheet: -1.99 (0.74), residues: 55 loop : -1.74 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 622 TYR 0.017 0.001 TYR A 620 PHE 0.011 0.001 PHE A 673 TRP 0.006 0.001 TRP A 326 HIS 0.003 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (10094) covalent geometry : angle 0.56160 / 0.28 (13645) hydrogen bonds : bond 0.03100 / 2.06 ( 356) hydrogen bonds : angle 4.55461 / 3.19 ( 1020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6617 (ttt90) cc_final: 0.6157 (mmt90) REVERT: A 76 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7774 (tp) REVERT: A 427 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 583 VAL cc_start: 0.8447 (t) cc_final: 0.8001 (m) REVERT: A 598 MET cc_start: 0.7348 (mtt) cc_final: 0.7059 (mtp) REVERT: A 660 ARG cc_start: 0.7420 (mmp80) cc_final: 0.7081 (mmt-90) REVERT: B 567 GLN cc_start: 0.8003 (mt0) cc_final: 0.7658 (mm-40) REVERT: B 602 LYS cc_start: 0.6891 (mttt) cc_final: 0.6541 (mttp) REVERT: B 615 MET cc_start: 0.8462 (mmm) cc_final: 0.8066 (mmt) outliers start: 11 outliers final: 7 residues processed: 149 average time/residue: 0.0969 time to fit residues: 20.0537 Evaluate side-chains 139 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.154542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113840 restraints weight = 13207.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109577 restraints weight = 11552.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110637 restraints weight = 14440.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112206 restraints weight = 9726.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112601 restraints weight = 7840.130| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10094 Z= 0.126 Angle : 0.565 10.853 13645 Z= 0.279 Chirality : 0.042 0.181 1523 Planarity : 0.003 0.047 1728 Dihedral : 5.941 53.653 1429 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.35 % Allowed : 17.40 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.23), residues: 1217 helix: -1.83 (0.17), residues: 802 sheet: -1.77 (0.73), residues: 57 loop : -1.81 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.013 0.001 TYR A 625 PHE 0.011 0.001 PHE A 673 TRP 0.013 0.001 TRP B 77 HIS 0.005 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10094) covalent geometry : angle 0.56459 / 0.28 (13645) hydrogen bonds : bond 0.03199 / 2.13 ( 356) hydrogen bonds : angle 4.50608 / 3.14 ( 1020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6671 (ttt90) cc_final: 0.6176 (mmt90) REVERT: A 76 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7788 (tp) REVERT: A 427 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 583 VAL cc_start: 0.8442 (t) cc_final: 0.7988 (m) REVERT: A 598 MET cc_start: 0.7397 (mtt) cc_final: 0.7110 (mtp) REVERT: A 660 ARG cc_start: 0.7414 (mmp80) cc_final: 0.7041 (mmt-90) REVERT: B 567 GLN cc_start: 0.8126 (mt0) cc_final: 0.7777 (mm-40) REVERT: B 615 MET cc_start: 0.8372 (mmm) cc_final: 0.8016 (mmt) outliers start: 14 outliers final: 11 residues processed: 153 average time/residue: 0.0989 time to fit residues: 21.1775 Evaluate side-chains 146 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 40 optimal weight: 0.9980 chunk 68 optimal weight: 0.0770 chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 669 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118537 restraints weight = 13198.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115304 restraints weight = 10568.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116373 restraints weight = 12860.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118108 restraints weight = 8638.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118368 restraints weight = 7071.317| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10094 Z= 0.095 Angle : 0.546 10.170 13645 Z= 0.269 Chirality : 0.040 0.182 1523 Planarity : 0.003 0.051 1728 Dihedral : 5.639 44.088 1429 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.96 % Allowed : 18.85 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.24), residues: 1217 helix: -1.58 (0.17), residues: 810 sheet: -1.81 (0.73), residues: 58 loop : -1.75 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 622 TYR 0.010 0.001 TYR B 571 PHE 0.012 0.001 PHE A 673 TRP 0.024 0.001 TRP B 77 HIS 0.005 0.000 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (10094) covalent geometry : angle 0.54586 / 0.27 (13645) hydrogen bonds : bond 0.02739 / 1.85 ( 356) hydrogen bonds : angle 4.33058 / 3.01 ( 1020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6735 (ttt90) cc_final: 0.6180 (mmt90) REVERT: A 402 ILE cc_start: 0.8680 (pt) cc_final: 0.8391 (mt) REVERT: A 403 MET cc_start: 0.8304 (mmt) cc_final: 0.8025 (mmp) REVERT: A 427 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7046 (mt-10) REVERT: A 583 VAL cc_start: 0.8341 (t) cc_final: 0.7842 (m) REVERT: A 598 MET cc_start: 0.7251 (mtt) cc_final: 0.6963 (mtp) REVERT: A 660 ARG cc_start: 0.7234 (mmp80) cc_final: 0.6919 (mmt-90) REVERT: B 126 ASP cc_start: 0.7647 (p0) cc_final: 0.7157 (p0) REVERT: B 567 GLN cc_start: 0.8133 (mt0) cc_final: 0.7772 (mm-40) REVERT: B 602 LYS cc_start: 0.7051 (mttt) cc_final: 0.6731 (mttp) outliers start: 10 outliers final: 6 residues processed: 149 average time/residue: 0.0937 time to fit residues: 19.3321 Evaluate side-chains 139 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 57 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 0 optimal weight: 0.8980 chunk 89 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 95 optimal weight: 0.0670 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116149 restraints weight = 13009.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112757 restraints weight = 11614.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114242 restraints weight = 13387.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115086 restraints weight = 8839.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115603 restraints weight = 7914.991| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10094 Z= 0.090 Angle : 0.535 9.794 13645 Z= 0.264 Chirality : 0.040 0.184 1523 Planarity : 0.003 0.058 1728 Dihedral : 5.482 41.882 1429 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.87 % Allowed : 19.33 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.24), residues: 1217 helix: -1.36 (0.18), residues: 806 sheet: -1.81 (0.72), residues: 57 loop : -1.62 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 622 TYR 0.014 0.001 TYR A 625 PHE 0.009 0.001 PHE A 673 TRP 0.016 0.001 TRP B 77 HIS 0.005 0.000 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (10094) covalent geometry : angle 0.53530 / 0.26 (13645) hydrogen bonds : bond 0.02668 / 1.79 ( 356) hydrogen bonds : angle 4.21747 / 2.94 ( 1020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6715 (ttt90) cc_final: 0.6185 (mmt90) REVERT: A 75 LEU cc_start: 0.7899 (tt) cc_final: 0.7625 (tt) REVERT: A 76 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7381 (mm) REVERT: A 403 MET cc_start: 0.8324 (mmt) cc_final: 0.8023 (mmp) REVERT: A 427 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7146 (mt-10) REVERT: A 548 MET cc_start: 0.8322 (mmm) cc_final: 0.7988 (mmp) REVERT: A 583 VAL cc_start: 0.8292 (t) cc_final: 0.7817 (m) REVERT: A 598 MET cc_start: 0.7195 (mtt) cc_final: 0.6899 (mtp) REVERT: A 660 ARG cc_start: 0.7240 (mmp80) cc_final: 0.6641 (mmt-90) REVERT: B 126 ASP cc_start: 0.7588 (p0) cc_final: 0.7132 (p0) REVERT: B 567 GLN cc_start: 0.8152 (mt0) cc_final: 0.7806 (mm-40) REVERT: B 602 LYS cc_start: 0.7067 (mttt) cc_final: 0.6754 (mttp) REVERT: B 712 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7460 (tpt90) outliers start: 9 outliers final: 7 residues processed: 145 average time/residue: 0.0995 time to fit residues: 20.0569 Evaluate side-chains 140 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 103 optimal weight: 0.0020 chunk 91 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 GLN B 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115381 restraints weight = 13033.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111800 restraints weight = 12087.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113257 restraints weight = 12749.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113970 restraints weight = 8968.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114431 restraints weight = 8272.746| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10094 Z= 0.105 Angle : 0.545 9.840 13645 Z= 0.268 Chirality : 0.041 0.168 1523 Planarity : 0.003 0.058 1728 Dihedral : 5.519 42.216 1429 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.35 % Allowed : 19.52 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.24), residues: 1217 helix: -1.27 (0.18), residues: 812 sheet: -1.86 (0.72), residues: 57 loop : -1.73 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 622 TYR 0.012 0.001 TYR B 296 PHE 0.012 0.001 PHE A 71 TRP 0.015 0.001 TRP B 77 HIS 0.004 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10094) covalent geometry : angle 0.54523 / 0.27 (13645) hydrogen bonds : bond 0.02800 / 1.88 ( 356) hydrogen bonds : angle 4.21934 / 2.93 ( 1020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.229 Fit side-chains REVERT: A 69 ARG cc_start: 0.6595 (ttt90) cc_final: 0.6082 (mmt90) REVERT: A 75 LEU cc_start: 0.7712 (tt) cc_final: 0.7433 (tt) REVERT: A 403 MET cc_start: 0.8276 (mmt) cc_final: 0.8034 (mmp) REVERT: A 427 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7186 (mt-10) REVERT: A 548 MET cc_start: 0.8273 (mmm) cc_final: 0.7912 (mmp) REVERT: A 583 VAL cc_start: 0.8305 (t) cc_final: 0.7839 (m) REVERT: A 598 MET cc_start: 0.7187 (mtt) cc_final: 0.6903 (mtp) REVERT: A 660 ARG cc_start: 0.7241 (mmp80) cc_final: 0.6633 (mmt-90) REVERT: B 126 ASP cc_start: 0.7618 (p0) cc_final: 0.7190 (p0) REVERT: B 225 THR cc_start: 0.8387 (m) cc_final: 0.7941 (p) REVERT: B 567 GLN cc_start: 0.8129 (mt0) cc_final: 0.7781 (mm-40) REVERT: B 602 LYS cc_start: 0.7114 (mttt) cc_final: 0.6765 (mttp) REVERT: B 712 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7458 (tpt90) outliers start: 14 outliers final: 11 residues processed: 145 average time/residue: 0.0961 time to fit residues: 19.3471 Evaluate side-chains 141 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN B 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117217 restraints weight = 13017.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114303 restraints weight = 10558.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115418 restraints weight = 12619.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116966 restraints weight = 8661.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117276 restraints weight = 7155.572| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10094 Z= 0.104 Angle : 0.549 9.797 13645 Z= 0.270 Chirality : 0.041 0.181 1523 Planarity : 0.003 0.058 1728 Dihedral : 5.459 41.241 1429 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.06 % Allowed : 20.10 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.24), residues: 1217 helix: -1.15 (0.18), residues: 812 sheet: -1.93 (0.72), residues: 57 loop : -1.73 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 622 TYR 0.021 0.001 TYR A 620 PHE 0.010 0.001 PHE A 673 TRP 0.015 0.001 TRP B 77 HIS 0.006 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (10094) covalent geometry : angle 0.54876 / 0.27 (13645) hydrogen bonds : bond 0.02826 / 1.90 ( 356) hydrogen bonds : angle 4.17917 / 2.90 ( 1020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.269 Fit side-chains REVERT: A 69 ARG cc_start: 0.6477 (ttt90) cc_final: 0.5876 (mmt90) REVERT: A 75 LEU cc_start: 0.7716 (tt) cc_final: 0.7440 (tt) REVERT: A 403 MET cc_start: 0.8299 (mmt) cc_final: 0.8064 (mmp) REVERT: A 427 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7160 (mt-10) REVERT: A 548 MET cc_start: 0.8252 (mmm) cc_final: 0.8049 (mmp) REVERT: A 583 VAL cc_start: 0.8364 (t) cc_final: 0.7909 (m) REVERT: A 598 MET cc_start: 0.7185 (mtt) cc_final: 0.6915 (mtp) REVERT: A 660 ARG cc_start: 0.7242 (mmp80) cc_final: 0.6616 (mmt-90) REVERT: B 126 ASP cc_start: 0.7599 (p0) cc_final: 0.7161 (p0) REVERT: B 567 GLN cc_start: 0.8118 (mt0) cc_final: 0.7787 (mm-40) REVERT: B 602 LYS cc_start: 0.7110 (mttt) cc_final: 0.6757 (mttp) REVERT: B 712 ARG cc_start: 0.7675 (ttp80) cc_final: 0.7463 (tpt90) outliers start: 11 outliers final: 11 residues processed: 145 average time/residue: 0.0941 time to fit residues: 19.1792 Evaluate side-chains 145 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 68 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.0030 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 121 optimal weight: 0.0980 chunk 119 optimal weight: 0.0020 overall best weight: 0.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 502 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.160396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117718 restraints weight = 13139.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115669 restraints weight = 9849.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117104 restraints weight = 10759.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118320 restraints weight = 7352.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118668 restraints weight = 6426.780| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10094 Z= 0.090 Angle : 0.540 9.732 13645 Z= 0.264 Chirality : 0.040 0.177 1523 Planarity : 0.003 0.062 1728 Dihedral : 5.270 40.805 1429 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.67 % Allowed : 20.96 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.24), residues: 1217 helix: -0.86 (0.18), residues: 813 sheet: -1.91 (0.72), residues: 57 loop : -1.64 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 622 TYR 0.019 0.001 TYR A 620 PHE 0.010 0.001 PHE A 673 TRP 0.015 0.001 TRP B 77 HIS 0.006 0.000 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (10094) covalent geometry : angle 0.53980 / 0.26 (13645) hydrogen bonds : bond 0.02543 / 1.72 ( 356) hydrogen bonds : angle 4.09575 / 2.84 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1539.88 seconds wall clock time: 27 minutes 11.98 seconds (1631.98 seconds total)