Starting phenix.real_space_refine on Fri Sep 11 22:06:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qq5_4618/09_2026/6qq5_4618.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qq5_4618/09_2026/6qq5_4618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qq5_4618/09_2026/6qq5_4618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qq5_4618/09_2026/6qq5_4618.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qq5_4618/09_2026/6qq5_4618.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qq5_4618/09_2026/6qq5_4618.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qq5_4618/09_2026/6qq5_4618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qq5_4618/09_2026/6qq5_4618.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 6 7.16 5 S 46 5.16 5 C 7835 2.51 5 N 1970 2.21 5 O 1970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11829 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5825 Classifications: {'peptide': 738} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 5828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5828 Classifications: {'peptide': 738} Link IDs: {'PTRANS': 35, 'TRANS': 702} Chain breaks: 1 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.72, per 1000 atoms: 0.23 Number of scatterers: 11829 At special positions: 0 Unit cell: (75.97, 118.77, 108.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 Ca 2 19.99 S 46 16.00 O 1970 8.00 N 1970 7.00 C 7835 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 517.3 milliseconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 2 sheets defined 60.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.078A pdb=" N ILE A 12 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 64 through 69 removed outlier: 7.388A pdb=" N MET A 67 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 69 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 101 removed outlier: 4.339A pdb=" N LEU A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.887A pdb=" N LEU A 111 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 127 removed outlier: 3.604A pdb=" N ALA A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 160 removed outlier: 4.216A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.263A pdb=" N ARG A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 254 removed outlier: 3.652A pdb=" N LEU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 Processing helix chain 'A' and resid 282 through 304 removed outlier: 3.941A pdb=" N VAL A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.639A pdb=" N VAL A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 351 removed outlier: 3.898A pdb=" N ALA A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 390 removed outlier: 3.942A pdb=" N GLY A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 390 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 439 removed outlier: 3.768A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix removed outlier: 3.516A pdb=" N ARG A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.846A pdb=" N ALA A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.598A pdb=" N PHE A 466 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 492 through 508 removed outlier: 3.677A pdb=" N PHE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 520 Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.586A pdb=" N LEU A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.776A pdb=" N HIS A 537 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.963A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 559 Processing helix chain 'A' and resid 560 through 565 removed outlier: 4.198A pdb=" N VAL A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.608A pdb=" N MET A 583 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 584' Processing helix chain 'A' and resid 588 through 603 removed outlier: 4.588A pdb=" N VAL A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 removed outlier: 3.538A pdb=" N MET A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 removed outlier: 3.555A pdb=" N HIS A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.816A pdb=" N LEU A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 670 through 678 Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.846A pdb=" N SER A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 683' Processing helix chain 'A' and resid 683 through 697 Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.666A pdb=" N ARG A 703 " --> pdb=" O TRP A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 742 removed outlier: 4.629A pdb=" N VAL A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 18 removed outlier: 4.138A pdb=" N ILE B 12 " --> pdb=" O TRP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.753A pdb=" N TYR B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 63 removed outlier: 3.596A pdb=" N LEU B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 removed outlier: 7.347A pdb=" N MET B 67 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 69 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.786A pdb=" N HIS B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.841A pdb=" N LEU B 111 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.568A pdb=" N ALA B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.728A pdb=" N ALA B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 160 removed outlier: 3.789A pdb=" N GLN B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 199 removed outlier: 3.769A pdb=" N THR B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 254 removed outlier: 3.973A pdb=" N VAL B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 235 " --> pdb=" O MET B 231 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 253 " --> pdb=" O TRP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.619A pdb=" N LEU B 282 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 304 removed outlier: 3.993A pdb=" N VAL B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.548A pdb=" N VAL B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 350 removed outlier: 3.820A pdb=" N THR B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.935A pdb=" N ILE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 355' Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 370 through 385 removed outlier: 3.645A pdb=" N LEU B 376 " --> pdb=" O TRP B 372 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.733A pdb=" N ALA B 390 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 432 removed outlier: 3.539A pdb=" N GLY B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.534A pdb=" N LEU B 438 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 439 " --> pdb=" O VAL B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 439' Processing helix chain 'B' and resid 445 through 459 removed outlier: 3.705A pdb=" N GLY B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.554A pdb=" N PHE B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 492 through 508 removed outlier: 3.629A pdb=" N PHE B 496 " --> pdb=" O PHE B 492 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 497 " --> pdb=" O PHE B 493 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 removed outlier: 3.649A pdb=" N LEU B 521 " --> pdb=" O THR B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 removed outlier: 3.805A pdb=" N HIS B 537 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 555 removed outlier: 3.503A pdb=" N ALA B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 559 removed outlier: 3.506A pdb=" N GLU B 559 " --> pdb=" O SER B 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 559' Processing helix chain 'B' and resid 560 through 565 removed outlier: 3.536A pdb=" N ILE B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 565' Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.619A pdb=" N MET B 583 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 584' Processing helix chain 'B' and resid 588 through 603 removed outlier: 4.254A pdb=" N VAL B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 595 " --> pdb=" O MET B 591 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 597 " --> pdb=" O PHE B 593 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 610 removed outlier: 3.578A pdb=" N MET B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 removed outlier: 3.584A pdb=" N HIS B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.642A pdb=" N SER B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 683 " --> pdb=" O ILE B 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 678 through 683' Processing helix chain 'B' and resid 685 through 695 removed outlier: 3.623A pdb=" N PHE B 691 " --> pdb=" O GLY B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.627A pdb=" N ARG B 703 " --> pdb=" O TRP B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 742 removed outlier: 4.606A pdb=" N VAL B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET B 734 " --> pdb=" O GLY B 730 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 4.672A pdb=" N VAL A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41 removed outlier: 4.721A pdb=" N VAL B 40 " --> pdb=" O LEU B 48 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1329 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: 1.46 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 4901 1.38 - 1.55: 7199 1.55 - 1.71: 29 1.71 - 1.87: 88 1.87 - 2.04: 16 Bond restraints: 12233 Sorted by residual: bond pdb=" C THR A 276 " pdb=" N PRO A 277 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.62e+00 bond pdb=" C THR B 276 " pdb=" N PRO B 277 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.46e+00 bond pdb=" N ARG A 168 " pdb=" CA ARG A 168 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.48e-02 4.57e+03 3.31e+00 bond pdb=" CB GLN A 296 " pdb=" CG GLN A 296 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.11e+00 bond pdb=" N ARG B 168 " pdb=" CA ARG B 168 " ideal model delta sigma weight residual 1.462 1.486 -0.024 1.48e-02 4.57e+03 2.66e+00 ... (remaining 12228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 15851 2.03 - 4.05: 684 4.05 - 6.08: 138 6.08 - 8.10: 53 8.10 - 10.13: 22 Bond angle restraints: 16748 Sorted by residual: angle pdb=" C ALA A 163 " pdb=" N PRO A 164 " pdb=" CA PRO A 164 " ideal model delta sigma weight residual 118.85 128.43 -9.58 1.09e+00 8.42e-01 7.73e+01 angle pdb=" N VAL A 560 " pdb=" CA VAL A 560 " pdb=" C VAL A 560 " ideal model delta sigma weight residual 113.42 106.65 6.77 1.17e+00 7.31e-01 3.35e+01 angle pdb=" N ILE A 712 " pdb=" CA ILE A 712 " pdb=" C ILE A 712 " ideal model delta sigma weight residual 112.96 107.18 5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" N VAL B 560 " pdb=" CA VAL B 560 " pdb=" C VAL B 560 " ideal model delta sigma weight residual 113.42 107.22 6.20 1.17e+00 7.31e-01 2.81e+01 angle pdb=" C GLU A 407 " pdb=" N TYR A 408 " pdb=" CA TYR A 408 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 ... (remaining 16743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6067 17.66 - 35.32: 577 35.32 - 52.98: 117 52.98 - 70.64: 19 70.64 - 88.30: 14 Dihedral angle restraints: 6794 sinusoidal: 2602 harmonic: 4192 Sorted by residual: dihedral pdb=" CA PHE A 461 " pdb=" C PHE A 461 " pdb=" N TYR A 462 " pdb=" CA TYR A 462 " ideal model delta harmonic sigma weight residual 180.00 154.22 25.78 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA SER B 169 " pdb=" C SER B 169 " pdb=" N ARG B 170 " pdb=" CA ARG B 170 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ARG B 168 " pdb=" C ARG B 168 " pdb=" N SER B 169 " pdb=" CA SER B 169 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 6791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1226 0.052 - 0.104: 431 0.104 - 0.155: 91 0.155 - 0.207: 22 0.207 - 0.259: 4 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CA THR B 276 " pdb=" N THR B 276 " pdb=" C THR B 276 " pdb=" CB THR B 276 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA THR A 276 " pdb=" N THR A 276 " pdb=" C THR A 276 " pdb=" CB THR A 276 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA TRP A 215 " pdb=" N TRP A 215 " pdb=" C TRP A 215 " pdb=" CB TRP A 215 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1771 not shown) Planarity restraints: 2077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 546 " 0.049 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO A 547 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 547 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 547 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 546 " -0.044 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO B 547 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 547 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 547 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 588 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO B 589 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " 0.032 5.00e-02 4.00e+02 ... (remaining 2074 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 42 2.41 - 3.04: 6085 3.04 - 3.66: 17537 3.66 - 4.28: 26122 4.28 - 4.90: 44113 Nonbonded interactions: 93899 Sorted by model distance: nonbonded pdb=" CE1 HIS B 486 " pdb="FE FE B 803 " model vdw 1.792 2.480 nonbonded pdb=" CE1 HIS A 486 " pdb="FE FE A 803 " model vdw 1.815 2.480 nonbonded pdb=" ND1 HIS B 486 " pdb="FE FE B 803 " model vdw 1.946 2.340 nonbonded pdb=" ND1 HIS A 486 " pdb="FE FE A 803 " model vdw 1.948 2.340 nonbonded pdb=" NE2 HIS A 538 " pdb="FE FE A 803 " model vdw 2.078 2.340 ... (remaining 93894 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' selection = (chain 'B' and (resid 1 through 395 or (resid 396 and (name N or name CA or name \ C or name O or name CB )) or resid 397 through 804)) } 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: 0.740 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.040 Find NCS groups from input model: 0.200 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.008 0.282 12237 Z= 0.298 Angle : 1.071 10.130 16748 Z= 0.567 Chirality : 0.056 0.259 1774 Planarity : 0.007 0.073 2077 Dihedral : 14.963 88.295 4130 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: -6.09 (0.14), residues: 1468 helix: -4.06 (0.09), residues: 924 sheet: None (None), residues: 0 loop : -3.68 (0.21), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 186 TYR 0.019 0.002 TYR B 618 PHE 0.023 0.002 PHE A 635 TRP 0.024 0.002 TRP A 338 HIS 0.011 0.002 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.30 (12233) covalent geometry : angle 1.07086 / 0.57 (16748) hydrogen bonds : bond 0.24132 / 16.10 ( 460) hydrogen bonds : angle 8.27031 / 5.81 ( 1329) Misc. bond : bond 0.20180 / 10.35 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.368 Fit side-chains REVERT: A 164 PRO cc_start: 0.8514 (Cg_endo) cc_final: 0.8293 (Cg_exo) REVERT: A 177 GLU cc_start: 0.8463 (tp30) cc_final: 0.8245 (mm-30) REVERT: A 296 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 344 LEU cc_start: 0.8684 (mt) cc_final: 0.8445 (mt) REVERT: A 376 LEU cc_start: 0.8739 (tt) cc_final: 0.8268 (tp) REVERT: A 393 MET cc_start: 0.8425 (ttm) cc_final: 0.8018 (mtp) REVERT: A 445 LYS cc_start: 0.7814 (pttp) cc_final: 0.7571 (pptt) REVERT: A 490 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6817 (tm-30) REVERT: A 503 PHE cc_start: 0.8649 (t80) cc_final: 0.8431 (t80) REVERT: A 583 MET cc_start: 0.8871 (tpp) cc_final: 0.8593 (tpp) REVERT: A 584 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 734 MET cc_start: 0.8622 (tpp) cc_final: 0.7978 (tpp) REVERT: B 93 MET cc_start: 0.8003 (mmt) cc_final: 0.7699 (mmt) REVERT: B 186 ARG cc_start: 0.8161 (ptt-90) cc_final: 0.7783 (ptp-170) REVERT: B 393 MET cc_start: 0.8119 (ttm) cc_final: 0.7601 (mtp) REVERT: B 425 PHE cc_start: 0.8922 (t80) cc_final: 0.8553 (t80) REVERT: B 461 PHE cc_start: 0.9003 (m-80) cc_final: 0.8792 (m-80) REVERT: B 593 PHE cc_start: 0.9178 (m-10) cc_final: 0.8976 (m-10) REVERT: B 734 MET cc_start: 0.8699 (tpp) cc_final: 0.7931 (tpp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1092 time to fit residues: 36.9438 Evaluate side-chains 204 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 172 ASN A 279 GLN A 305 HIS A 331 HIS A 385 ASN A 473 HIS A 692 HIS B 172 ASN B 305 HIS B 385 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.128442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.107739 restraints weight = 15871.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.108873 restraints weight = 31528.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.107123 restraints weight = 20764.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.108011 restraints weight = 23272.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.107627 restraints weight = 18693.080| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 12237 Z= 0.138 Angle : 0.698 13.608 16748 Z= 0.337 Chirality : 0.041 0.154 1774 Planarity : 0.005 0.055 2077 Dihedral : 7.489 75.287 1636 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.38 % Allowed : 9.77 % Favored : 88.85 % 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: -4.29 (0.18), residues: 1468 helix: -2.59 (0.14), residues: 910 sheet: None (None), residues: 0 loop : -3.09 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 513 TYR 0.018 0.001 TYR B 406 PHE 0.011 0.001 PHE B 503 TRP 0.022 0.001 TRP B 338 HIS 0.006 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (12233) covalent geometry : angle 0.69756 / 0.34 (16748) hydrogen bonds : bond 0.05085 / 3.34 ( 460) hydrogen bonds : angle 4.86072 / 3.42 ( 1329) Misc. bond : bond 0.14011 / 7.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 296 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 344 LEU cc_start: 0.8471 (mt) cc_final: 0.8250 (mt) REVERT: A 393 MET cc_start: 0.8110 (ttm) cc_final: 0.7716 (ttm) REVERT: A 445 LYS cc_start: 0.7722 (pttp) cc_final: 0.7459 (pptt) REVERT: A 490 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6642 (tm-30) REVERT: A 734 MET cc_start: 0.8470 (tpp) cc_final: 0.7859 (tpp) REVERT: B 425 PHE cc_start: 0.8676 (t80) cc_final: 0.8127 (t80) REVERT: B 490 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7089 (tm-30) REVERT: B 569 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7614 (tt0) outliers start: 16 outliers final: 10 residues processed: 218 average time/residue: 0.1010 time to fit residues: 32.0258 Evaluate side-chains 199 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 515 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 97 optimal weight: 0.3980 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 0.0020 chunk 89 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 HIS B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.136610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.115842 restraints weight = 15549.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.117413 restraints weight = 31808.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.116371 restraints weight = 18571.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.116635 restraints weight = 18609.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.116437 restraints weight = 15716.213| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 12237 Z= 0.113 Angle : 0.635 12.131 16748 Z= 0.304 Chirality : 0.039 0.149 1774 Planarity : 0.004 0.050 2077 Dihedral : 7.008 74.865 1636 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.64 % Allowed : 12.19 % Favored : 86.17 % 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: -3.22 (0.20), residues: 1468 helix: -1.65 (0.16), residues: 894 sheet: None (None), residues: 0 loop : -2.81 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 513 TYR 0.014 0.001 TYR B 324 PHE 0.025 0.001 PHE A 503 TRP 0.016 0.001 TRP B 338 HIS 0.012 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.11 (12233) covalent geometry : angle 0.63465 / 0.30 (16748) hydrogen bonds : bond 0.04000 / 2.62 ( 460) hydrogen bonds : angle 4.33582 / 3.03 ( 1329) Misc. bond : bond 0.08218 / 4.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.455 Fit side-chains REVERT: A 445 LYS cc_start: 0.7662 (pttp) cc_final: 0.7430 (pptt) REVERT: A 490 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6635 (tm-30) REVERT: A 555 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7892 (t80) REVERT: A 734 MET cc_start: 0.8430 (tpp) cc_final: 0.7861 (tpp) REVERT: B 31 ARG cc_start: 0.7880 (ptt180) cc_final: 0.7619 (ptt180) REVERT: B 569 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7501 (tt0) REVERT: B 734 MET cc_start: 0.8462 (tpp) cc_final: 0.8016 (tpp) outliers start: 19 outliers final: 12 residues processed: 205 average time/residue: 0.0964 time to fit residues: 29.2344 Evaluate side-chains 196 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 515 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 331 HIS A 473 HIS B 89 HIS B 585 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.130190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.114895 restraints weight = 15913.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.113417 restraints weight = 24210.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.110434 restraints weight = 21858.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.111320 restraints weight = 23908.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.110662 restraints weight = 17392.972| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.167 12237 Z= 0.208 Angle : 0.711 15.780 16748 Z= 0.333 Chirality : 0.044 0.167 1774 Planarity : 0.004 0.050 2077 Dihedral : 7.118 74.055 1636 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.25 % Allowed : 14.95 % Favored : 82.80 % 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: -2.88 (0.21), residues: 1468 helix: -1.42 (0.17), residues: 916 sheet: None (None), residues: 0 loop : -2.62 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 513 TYR 0.028 0.002 TYR B 362 PHE 0.020 0.002 PHE A 503 TRP 0.018 0.001 TRP B 426 HIS 0.008 0.002 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 (12233) covalent geometry : angle 0.71125 / 0.33 (16748) hydrogen bonds : bond 0.04681 / 3.05 ( 460) hydrogen bonds : angle 4.38640 / 3.07 ( 1329) Misc. bond : bond 0.13414 / 6.79 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.443 Fit side-chains REVERT: A 393 MET cc_start: 0.8152 (ttp) cc_final: 0.7867 (ttm) REVERT: A 445 LYS cc_start: 0.7685 (pttp) cc_final: 0.7282 (pptt) REVERT: A 490 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6793 (tm-30) REVERT: A 555 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8141 (t80) REVERT: A 734 MET cc_start: 0.8461 (tpp) cc_final: 0.7854 (tpp) REVERT: B 31 ARG cc_start: 0.7943 (ptt180) cc_final: 0.7691 (ptt180) REVERT: B 344 LEU cc_start: 0.8558 (mt) cc_final: 0.8107 (mt) REVERT: B 490 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7084 (tm-30) REVERT: B 569 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7615 (tt0) REVERT: B 678 MET cc_start: 0.8915 (ptp) cc_final: 0.8692 (ptm) REVERT: B 734 MET cc_start: 0.8493 (tpp) cc_final: 0.8053 (tpp) outliers start: 26 outliers final: 23 residues processed: 200 average time/residue: 0.0867 time to fit residues: 26.0380 Evaluate side-chains 200 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 544 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.127765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.110116 restraints weight = 16035.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109070 restraints weight = 29543.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.107482 restraints weight = 20600.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.108063 restraints weight = 24487.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.107457 restraints weight = 18603.521| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 12237 Z= 0.116 Angle : 0.625 12.504 16748 Z= 0.298 Chirality : 0.040 0.139 1774 Planarity : 0.004 0.049 2077 Dihedral : 6.857 75.736 1636 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.51 % Allowed : 15.47 % Favored : 82.02 % 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: -2.42 (0.21), residues: 1468 helix: -0.99 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -2.51 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 513 TYR 0.018 0.001 TYR B 324 PHE 0.011 0.001 PHE B 593 TRP 0.033 0.001 TRP B 426 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (12233) covalent geometry : angle 0.62535 / 0.30 (16748) hydrogen bonds : bond 0.03825 / 2.50 ( 460) hydrogen bonds : angle 4.08870 / 2.86 ( 1329) Misc. bond : bond 0.07681 / 3.93 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.275 Fit side-chains REVERT: A 445 LYS cc_start: 0.7701 (pttp) cc_final: 0.7252 (pptt) REVERT: A 555 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7999 (t80) REVERT: A 734 MET cc_start: 0.8416 (tpp) cc_final: 0.7841 (tpp) REVERT: B 31 ARG cc_start: 0.7844 (ptt180) cc_final: 0.7576 (ptt180) REVERT: B 344 LEU cc_start: 0.8608 (mt) cc_final: 0.8126 (mt) REVERT: B 461 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.7831 (t80) REVERT: B 734 MET cc_start: 0.8423 (tpp) cc_final: 0.7969 (tpp) outliers start: 29 outliers final: 17 residues processed: 195 average time/residue: 0.0952 time to fit residues: 27.6745 Evaluate side-chains 193 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 HIS ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.133855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.116667 restraints weight = 15717.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.116444 restraints weight = 28410.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.114771 restraints weight = 19522.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.115441 restraints weight = 23568.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.114604 restraints weight = 16645.662| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 12237 Z= 0.122 Angle : 0.623 12.359 16748 Z= 0.295 Chirality : 0.040 0.137 1774 Planarity : 0.004 0.048 2077 Dihedral : 6.770 75.412 1636 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.51 % Allowed : 16.51 % Favored : 80.99 % 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: -2.09 (0.22), residues: 1468 helix: -0.73 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.38 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 471 TYR 0.025 0.001 TYR B 362 PHE 0.017 0.001 PHE B 503 TRP 0.032 0.001 TRP B 426 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.12 (12233) covalent geometry : angle 0.62299 / 0.29 (16748) hydrogen bonds : bond 0.03675 / 2.40 ( 460) hydrogen bonds : angle 3.96956 / 2.78 ( 1329) Misc. bond : bond 0.07825 / 3.98 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.386 Fit side-chains REVERT: A 393 MET cc_start: 0.8121 (ttp) cc_final: 0.7720 (ttm) REVERT: A 445 LYS cc_start: 0.7693 (pttp) cc_final: 0.7181 (pptt) REVERT: A 529 LEU cc_start: 0.9032 (tp) cc_final: 0.8744 (tp) REVERT: A 555 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7987 (t80) REVERT: A 734 MET cc_start: 0.8427 (tpp) cc_final: 0.7843 (tpp) REVERT: B 31 ARG cc_start: 0.7895 (ptt180) cc_final: 0.7610 (ptt180) REVERT: B 344 LEU cc_start: 0.8581 (mt) cc_final: 0.8214 (mt) REVERT: B 461 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.7834 (t80) REVERT: B 734 MET cc_start: 0.8369 (tpp) cc_final: 0.7901 (tpp) outliers start: 29 outliers final: 22 residues processed: 191 average time/residue: 0.0976 time to fit residues: 27.8783 Evaluate side-chains 191 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 695 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 90 optimal weight: 6.9990 chunk 20 optimal weight: 0.0030 chunk 108 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 78 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 473 HIS ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.130794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.111972 restraints weight = 15822.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.111500 restraints weight = 29808.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109226 restraints weight = 19940.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.109804 restraints weight = 22126.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.109414 restraints weight = 16139.641| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12237 Z= 0.104 Angle : 0.602 11.067 16748 Z= 0.287 Chirality : 0.039 0.136 1774 Planarity : 0.004 0.047 2077 Dihedral : 6.622 76.803 1636 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.07 % Allowed : 17.03 % Favored : 80.90 % 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: -1.79 (0.22), residues: 1468 helix: -0.49 (0.18), residues: 892 sheet: None (None), residues: 0 loop : -2.26 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 168 TYR 0.021 0.001 TYR A 362 PHE 0.022 0.001 PHE A 503 TRP 0.033 0.001 TRP B 426 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.10 (12233) covalent geometry : angle 0.60238 / 0.29 (16748) hydrogen bonds : bond 0.03282 / 2.14 ( 460) hydrogen bonds : angle 3.81134 / 2.67 ( 1329) Misc. bond : bond 0.05646 / 2.88 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.396 Fit side-chains REVERT: A 177 GLU cc_start: 0.7423 (tp30) cc_final: 0.7024 (pp20) REVERT: A 344 LEU cc_start: 0.8252 (mt) cc_final: 0.7930 (mt) REVERT: A 445 LYS cc_start: 0.7756 (pttp) cc_final: 0.7199 (pptt) REVERT: A 734 MET cc_start: 0.8406 (tpp) cc_final: 0.7844 (tpp) REVERT: B 31 ARG cc_start: 0.7893 (ptt180) cc_final: 0.7622 (ptt180) REVERT: B 344 LEU cc_start: 0.8510 (mt) cc_final: 0.8259 (mt) REVERT: B 348 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.7983 (tt) REVERT: B 376 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8139 (tp) REVERT: B 461 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7798 (t80) outliers start: 24 outliers final: 15 residues processed: 193 average time/residue: 0.0932 time to fit residues: 27.1202 Evaluate side-chains 186 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 515 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 31 optimal weight: 0.0370 chunk 123 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN A 473 HIS ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.134031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.116869 restraints weight = 15639.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.117033 restraints weight = 28519.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.115621 restraints weight = 20050.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.116191 restraints weight = 21750.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.115284 restraints weight = 16202.305| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 12237 Z= 0.151 Angle : 0.647 12.969 16748 Z= 0.306 Chirality : 0.042 0.150 1774 Planarity : 0.004 0.045 2077 Dihedral : 6.718 74.854 1636 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.33 % Allowed : 17.11 % Favored : 80.55 % 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: -1.73 (0.22), residues: 1468 helix: -0.47 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -2.18 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 90 TYR 0.025 0.001 TYR B 362 PHE 0.018 0.001 PHE B 503 TRP 0.036 0.001 TRP B 426 HIS 0.007 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.15 (12233) covalent geometry : angle 0.64654 / 0.31 (16748) hydrogen bonds : bond 0.03808 / 2.49 ( 460) hydrogen bonds : angle 3.91699 / 2.73 ( 1329) Misc. bond : bond 0.09273 / 4.73 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.318 Fit side-chains REVERT: A 393 MET cc_start: 0.8119 (ttp) cc_final: 0.7766 (mtp) REVERT: A 445 LYS cc_start: 0.7743 (pttp) cc_final: 0.7230 (pptt) REVERT: A 461 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7934 (t80) REVERT: A 515 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8333 (mtm) REVERT: A 734 MET cc_start: 0.8320 (tpp) cc_final: 0.7749 (tpp) REVERT: B 31 ARG cc_start: 0.7872 (ptt180) cc_final: 0.7593 (ptt180) REVERT: B 344 LEU cc_start: 0.8590 (mt) cc_final: 0.8332 (mt) REVERT: B 425 PHE cc_start: 0.8631 (t80) cc_final: 0.8059 (t80) REVERT: B 461 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7883 (t80) outliers start: 27 outliers final: 21 residues processed: 189 average time/residue: 0.0857 time to fit residues: 24.3891 Evaluate side-chains 191 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 695 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 144 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 0.0060 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.130078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.111784 restraints weight = 15691.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.111017 restraints weight = 29409.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.108520 restraints weight = 24350.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.109349 restraints weight = 25199.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.109064 restraints weight = 17686.771| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 12237 Z= 0.118 Angle : 0.630 10.555 16748 Z= 0.299 Chirality : 0.040 0.134 1774 Planarity : 0.004 0.045 2077 Dihedral : 6.621 77.280 1636 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.25 % Allowed : 17.55 % Favored : 80.21 % 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: -1.54 (0.22), residues: 1468 helix: -0.29 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -2.12 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 90 TYR 0.021 0.001 TYR A 362 PHE 0.030 0.001 PHE A 503 TRP 0.039 0.001 TRP B 426 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 (12233) covalent geometry : angle 0.62969 / 0.30 (16748) hydrogen bonds : bond 0.03533 / 2.33 ( 460) hydrogen bonds : angle 3.85878 / 2.70 ( 1329) Misc. bond : bond 0.07173 / 3.65 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.324 Fit side-chains REVERT: A 177 GLU cc_start: 0.7433 (tp30) cc_final: 0.6987 (pp20) REVERT: A 425 PHE cc_start: 0.8650 (t80) cc_final: 0.8078 (t80) REVERT: A 445 LYS cc_start: 0.7810 (pttp) cc_final: 0.7157 (pptt) REVERT: A 461 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7935 (t80) REVERT: A 515 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8416 (mtm) REVERT: A 734 MET cc_start: 0.8373 (tpp) cc_final: 0.7833 (tpp) REVERT: B 31 ARG cc_start: 0.7899 (ptt180) cc_final: 0.7648 (ptt180) REVERT: B 298 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8174 (mm) REVERT: B 376 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8101 (tp) REVERT: B 425 PHE cc_start: 0.8630 (t80) cc_final: 0.8062 (t80) REVERT: B 461 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.7945 (t80) outliers start: 26 outliers final: 19 residues processed: 184 average time/residue: 0.1008 time to fit residues: 27.8982 Evaluate side-chains 190 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 549 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 106 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 137 optimal weight: 0.1980 chunk 144 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.126471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.107853 restraints weight = 16119.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.107195 restraints weight = 30445.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.104239 restraints weight = 25982.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.104847 restraints weight = 28049.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.104412 restraints weight = 18430.021| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 12237 Z= 0.197 Angle : 0.695 12.819 16748 Z= 0.328 Chirality : 0.044 0.182 1774 Planarity : 0.004 0.043 2077 Dihedral : 6.827 74.950 1636 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.25 % Allowed : 17.72 % Favored : 80.03 % 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: -1.68 (0.22), residues: 1468 helix: -0.46 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.020 0.001 TYR A 618 PHE 0.022 0.001 PHE B 503 TRP 0.042 0.001 TRP B 426 HIS 0.008 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.20 (12233) covalent geometry : angle 0.69541 / 0.33 (16748) hydrogen bonds : bond 0.04255 / 2.79 ( 460) hydrogen bonds : angle 4.07184 / 2.85 ( 1329) Misc. bond : bond 0.11602 / 5.89 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.505 Fit side-chains REVERT: A 445 LYS cc_start: 0.7684 (pttp) cc_final: 0.7000 (pptt) REVERT: A 461 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8067 (t80) REVERT: A 515 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8563 (mtm) REVERT: A 555 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7972 (t80) REVERT: A 734 MET cc_start: 0.8360 (tpp) cc_final: 0.7804 (tpp) REVERT: B 31 ARG cc_start: 0.7940 (ptt180) cc_final: 0.7690 (ptt180) REVERT: B 298 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8243 (mm) REVERT: B 344 LEU cc_start: 0.8551 (mt) cc_final: 0.8287 (mt) REVERT: B 461 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8052 (t80) REVERT: B 555 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7950 (t80) outliers start: 26 outliers final: 19 residues processed: 185 average time/residue: 0.0961 time to fit residues: 26.6399 Evaluate side-chains 192 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 555 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 119 optimal weight: 3.9990 chunk 111 optimal weight: 0.0070 chunk 110 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 54 optimal weight: 0.0770 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.129991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.111405 restraints weight = 15912.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.110320 restraints weight = 30345.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107875 restraints weight = 24370.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.108547 restraints weight = 25144.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.107945 restraints weight = 17322.766| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 12237 Z= 0.114 Angle : 0.637 10.887 16748 Z= 0.301 Chirality : 0.040 0.153 1774 Planarity : 0.004 0.045 2077 Dihedral : 6.588 76.535 1636 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.90 % Allowed : 18.24 % Favored : 79.86 % 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: -1.44 (0.23), residues: 1468 helix: -0.20 (0.18), residues: 882 sheet: None (None), residues: 0 loop : -2.11 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 90 TYR 0.016 0.001 TYR B 324 PHE 0.010 0.001 PHE A 24 TRP 0.035 0.001 TRP B 426 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.11 (12233) covalent geometry : angle 0.63698 / 0.30 (16748) hydrogen bonds : bond 0.03425 / 2.26 ( 460) hydrogen bonds : angle 3.87265 / 2.71 ( 1329) Misc. bond : bond 0.06956 / 3.55 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1529.25 seconds wall clock time: 27 minutes 9.02 seconds (1629.02 seconds total)