Starting phenix.real_space_refine on Wed Mar 4 07:35:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qq5_4618/03_2026/6qq5_4618.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qq5_4618/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6qq5_4618/03_2026/6qq5_4618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qq5_4618/03_2026/6qq5_4618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qq5_4618/03_2026/6qq5_4618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qq5_4618/03_2026/6qq5_4618.map" } 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-dev-5986/lib/python3.9/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: 3.03, per 1000 atoms: 0.26 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: 0.97 Conformation dependent library (CDL) restraints added in 527.5 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: 0.35 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: 1.68 Time building geometry restraints manager: 1.31 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.880 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 covalent geometry : bond 0.00709 (12233) covalent geometry : angle 1.07086 (16748) hydrogen bonds : bond 0.24132 ( 460) hydrogen bonds : angle 8.27031 ( 1329) Misc. bond : bond 0.20180 ( 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 : 0.383 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: 0.8446 (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: 0.8592 (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: 0.7698 (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: 0.1233 time to fit residues: 41.2352 Evaluate side-chains 205 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 188 GLN B 305 HIS B 385 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.128963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.108264 restraints weight = 15878.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.109271 restraints weight = 31836.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.107656 restraints weight = 21533.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.108403 restraints weight = 23399.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.107803 restraints weight = 19736.276| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 12237 Z= 0.135 Angle : 0.691 13.146 16748 Z= 0.335 Chirality : 0.041 0.156 1774 Planarity : 0.005 0.054 2077 Dihedral : 7.427 75.330 1636 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.38 % Allowed : 9.85 % Favored : 88.76 % 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: -2.60 (0.14), residues: 910 sheet: None (None), residues: 0 loop : -3.06 (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 0.013 0.001 PHE B 503 TRP 0.023 0.001 TRP B 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00325 (12233) covalent geometry : angle 0.69144 (16748) hydrogen bonds : bond 0.04958 ( 460) hydrogen bonds : angle 4.83661 ( 1329) Misc. bond : bond 0.12696 ( 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 231 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 344 LEU cc_start: 0.8466 (mt) cc_final: 0.8246 (mt) REVERT: A 393 MET cc_start: 0.8150 (ttm) cc_final: 0.7704 (ttm) REVERT: A 445 LYS cc_start: 0.7703 (pttp) cc_final: 0.7472 (pptt) REVERT: A 490 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6630 (tm-30) REVERT: A 584 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 734 MET cc_start: 0.8466 (tpp) cc_final: 0.7853 (tpp) REVERT: B 425 PHE cc_start: 0.8676 (t80) cc_final: 0.8115 (t80) REVERT: B 490 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7063 (tm-30) REVERT: B 569 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7615 (tt0) outliers start: 16 outliers final: 10 residues processed: 219 average time/residue: 0.1088 time to fit residues: 34.6465 Evaluate side-chains 201 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 0.0000 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A 331 HIS A 473 HIS B 62 GLN B 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.128375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.108520 restraints weight = 16016.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.108402 restraints weight = 30478.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.105956 restraints weight = 21347.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.106692 restraints weight = 22531.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.106002 restraints weight = 17712.680| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 12237 Z= 0.130 Angle : 0.653 13.740 16748 Z= 0.312 Chirality : 0.040 0.147 1774 Planarity : 0.004 0.051 2077 Dihedral : 7.120 74.208 1636 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.47 % Allowed : 12.79 % Favored : 85.74 % 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: -3.40 (0.20), residues: 1468 helix: -1.81 (0.16), residues: 910 sheet: None (None), residues: 0 loop : -2.87 (0.24), residues: 558 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 0.022 0.001 PHE A 503 TRP 0.016 0.001 TRP B 338 HIS 0.016 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00323 (12233) covalent geometry : angle 0.65320 (16748) hydrogen bonds : bond 0.04276 ( 460) hydrogen bonds : angle 4.42700 ( 1329) Misc. bond : bond 0.10407 ( 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 212 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.423 Fit side-chains REVERT: A 445 LYS cc_start: 0.7688 (pttp) cc_final: 0.7428 (pptt) REVERT: A 490 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6670 (tm-30) REVERT: A 555 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7872 (t80) REVERT: A 734 MET cc_start: 0.8450 (tpp) cc_final: 0.7890 (tpp) REVERT: B 31 ARG cc_start: 0.7948 (ptt180) cc_final: 0.7701 (ptt180) REVERT: B 296 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8415 (tm-30) REVERT: B 425 PHE cc_start: 0.8656 (t80) cc_final: 0.8078 (t80) REVERT: B 490 GLU cc_start: 0.7333 (tm-30) cc_final: 0.7035 (tm-30) REVERT: B 569 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7550 (tt0) REVERT: B 734 MET cc_start: 0.8514 (tpp) cc_final: 0.8110 (tpp) outliers start: 17 outliers final: 10 residues processed: 202 average time/residue: 0.1082 time to fit residues: 32.0027 Evaluate side-chains 192 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 318 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 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: 2.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 473 HIS B 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.125277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.107268 restraints weight = 16231.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.105823 restraints weight = 31458.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.103300 restraints weight = 26165.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.104092 restraints weight = 27527.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.103678 restraints weight = 18670.660| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 12237 Z= 0.185 Angle : 0.690 14.989 16748 Z= 0.325 Chirality : 0.043 0.159 1774 Planarity : 0.004 0.050 2077 Dihedral : 7.119 72.716 1636 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.25 % Allowed : 14.52 % Favored : 83.23 % 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: -2.91 (0.21), residues: 1468 helix: -1.44 (0.17), residues: 914 sheet: None (None), residues: 0 loop : -2.64 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 513 TYR 0.031 0.001 TYR B 362 PHE 0.029 0.001 PHE A 503 TRP 0.030 0.001 TRP B 426 HIS 0.008 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00460 (12233) covalent geometry : angle 0.69015 (16748) hydrogen bonds : bond 0.04536 ( 460) hydrogen bonds : angle 4.37619 ( 1329) Misc. bond : bond 0.12313 ( 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 : 0.419 Fit side-chains revert: symmetry clash REVERT: A 393 MET cc_start: 0.8120 (ttp) cc_final: 0.7852 (ttm) REVERT: A 445 LYS cc_start: 0.7703 (pttp) cc_final: 0.7245 (pptt) REVERT: A 490 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6741 (tm-30) REVERT: A 555 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.8096 (t80) REVERT: A 734 MET cc_start: 0.8432 (tpp) cc_final: 0.7834 (tpp) REVERT: B 31 ARG cc_start: 0.7939 (ptt180) cc_final: 0.7671 (ptt180) REVERT: B 490 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7101 (tm-30) REVERT: B 569 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7600 (tt0) REVERT: B 734 MET cc_start: 0.8490 (tpp) cc_final: 0.7974 (tpp) outliers start: 26 outliers final: 22 residues processed: 199 average time/residue: 0.1082 time to fit residues: 31.8705 Evaluate side-chains 204 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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 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 318 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 27 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.127008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.109493 restraints weight = 16161.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.108478 restraints weight = 31309.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.106737 restraints weight = 19404.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.107036 restraints weight = 21703.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.106601 restraints weight = 16412.339| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 12237 Z= 0.151 Angle : 0.650 12.974 16748 Z= 0.308 Chirality : 0.041 0.138 1774 Planarity : 0.004 0.049 2077 Dihedral : 6.955 75.371 1636 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.28 % Allowed : 15.04 % Favored : 81.68 % 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: -2.57 (0.21), residues: 1468 helix: -1.15 (0.17), residues: 908 sheet: None (None), residues: 0 loop : -2.51 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 513 TYR 0.023 0.001 TYR A 362 PHE 0.014 0.001 PHE B 593 TRP 0.023 0.001 TRP B 426 HIS 0.007 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00383 (12233) covalent geometry : angle 0.65038 (16748) hydrogen bonds : bond 0.04104 ( 460) hydrogen bonds : angle 4.19921 ( 1329) Misc. bond : bond 0.10550 ( 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 222 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.419 Fit side-chains REVERT: A 445 LYS cc_start: 0.7595 (pttp) cc_final: 0.7124 (pptt) REVERT: A 490 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6724 (tm-30) REVERT: A 555 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8056 (t80) REVERT: A 734 MET cc_start: 0.8404 (tpp) cc_final: 0.7827 (tpp) REVERT: B 31 ARG cc_start: 0.7890 (ptt180) cc_final: 0.7630 (ptt180) REVERT: B 490 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7046 (tm-30) REVERT: B 734 MET cc_start: 0.8435 (tpp) cc_final: 0.7940 (tpp) outliers start: 38 outliers final: 27 residues processed: 201 average time/residue: 0.0984 time to fit residues: 29.5593 Evaluate side-chains 200 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 239 VAL 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 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 71 SER Chi-restraints excluded: chain B residue 93 MET 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 290 VAL 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 515 MET Chi-restraints excluded: chain B residue 544 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 128 optimal weight: 0.2980 chunk 30 optimal weight: 0.4980 chunk 90 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 59 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3352 r_free = 0.3352 target = 0.130182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.112728 restraints weight = 15914.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.112680 restraints weight = 28862.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.111428 restraints weight = 18113.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.111585 restraints weight = 23691.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.111113 restraints weight = 15935.185| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12237 Z= 0.104 Angle : 0.619 11.032 16748 Z= 0.293 Chirality : 0.039 0.146 1774 Planarity : 0.004 0.048 2077 Dihedral : 6.710 77.499 1636 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.16 % Allowed : 16.59 % Favored : 81.24 % 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: -2.08 (0.22), residues: 1468 helix: -0.72 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.36 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 168 TYR 0.026 0.001 TYR B 362 PHE 0.023 0.001 PHE B 503 TRP 0.028 0.001 TRP B 426 HIS 0.004 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00255 (12233) covalent geometry : angle 0.61932 (16748) hydrogen bonds : bond 0.03395 ( 460) hydrogen bonds : angle 3.91691 ( 1329) Misc. bond : bond 0.05818 ( 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 208 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.417 Fit side-chains REVERT: A 393 MET cc_start: 0.8083 (ttp) cc_final: 0.7692 (ttm) REVERT: A 445 LYS cc_start: 0.7725 (pttp) cc_final: 0.7252 (pptt) REVERT: A 490 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6691 (tm-30) REVERT: A 734 MET cc_start: 0.8416 (tpp) cc_final: 0.7859 (tpp) REVERT: B 31 ARG cc_start: 0.7893 (ptt180) cc_final: 0.7604 (ptt180) REVERT: B 191 HIS cc_start: 0.8286 (m-70) cc_final: 0.7874 (m170) REVERT: B 348 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8134 (tt) REVERT: B 376 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8054 (tp) REVERT: B 458 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8353 (mm) REVERT: B 461 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7827 (t80) outliers start: 25 outliers final: 10 residues processed: 192 average time/residue: 0.0995 time to fit residues: 28.4189 Evaluate side-chains 184 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU 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 515 MET Chi-restraints excluded: chain A residue 549 MET 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 458 ILE Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 515 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 90 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3325 r_free = 0.3325 target = 0.128101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.110506 restraints weight = 15965.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.110084 restraints weight = 29838.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.107098 restraints weight = 25890.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.107971 restraints weight = 27214.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.107668 restraints weight = 18636.545| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 12237 Z= 0.147 Angle : 0.646 13.149 16748 Z= 0.304 Chirality : 0.042 0.147 1774 Planarity : 0.004 0.047 2077 Dihedral : 6.777 74.426 1636 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.59 % Allowed : 16.94 % Favored : 80.47 % 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: -1.97 (0.22), residues: 1468 helix: -0.65 (0.18), residues: 892 sheet: None (None), residues: 0 loop : -2.29 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 471 TYR 0.017 0.001 TYR B 324 PHE 0.021 0.001 PHE A 503 TRP 0.043 0.001 TRP B 426 HIS 0.007 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00374 (12233) covalent geometry : angle 0.64551 (16748) hydrogen bonds : bond 0.03822 ( 460) hydrogen bonds : angle 3.98391 ( 1329) Misc. bond : bond 0.09240 ( 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 201 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 393 MET cc_start: 0.8167 (ttp) cc_final: 0.7734 (ttm) REVERT: A 445 LYS cc_start: 0.7646 (pttp) cc_final: 0.7116 (pptt) REVERT: A 490 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6759 (tm-30) REVERT: A 515 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8363 (mtm) REVERT: A 555 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7963 (t80) REVERT: A 734 MET cc_start: 0.8380 (tpp) cc_final: 0.7765 (tpp) REVERT: B 31 ARG cc_start: 0.7915 (ptt180) cc_final: 0.7634 (ptt180) REVERT: B 376 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8589 (tp) REVERT: B 425 PHE cc_start: 0.8633 (t80) cc_final: 0.8042 (t80) REVERT: B 461 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.7876 (t80) outliers start: 30 outliers final: 18 residues processed: 189 average time/residue: 0.1030 time to fit residues: 29.1103 Evaluate side-chains 191 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 230 VAL Chi-restraints excluded: chain A residue 325 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 448 LEU Chi-restraints excluded: chain A residue 478 GLU 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 180 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 SER 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 544 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 31 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 30 optimal weight: 0.0040 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3342 r_free = 0.3342 target = 0.129404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.110639 restraints weight = 15910.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.110423 restraints weight = 29700.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.107979 restraints weight = 19954.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.108571 restraints weight = 21658.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.108029 restraints weight = 16538.815| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2569 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 : 0.627 11.746 16748 Z= 0.295 Chirality : 0.040 0.176 1774 Planarity : 0.004 0.047 2077 Dihedral : 6.660 76.216 1636 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.07 % Allowed : 17.80 % Favored : 80.12 % 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: -1.85 (0.22), residues: 1468 helix: -0.58 (0.18), residues: 908 sheet: None (None), residues: 0 loop : -2.23 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 471 TYR 0.016 0.001 TYR B 324 PHE 0.017 0.001 PHE B 503 TRP 0.042 0.001 TRP B 426 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00286 (12233) covalent geometry : angle 0.62748 (16748) hydrogen bonds : bond 0.03509 ( 460) hydrogen bonds : angle 3.88643 ( 1329) Misc. bond : bond 0.06963 ( 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 201 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.397 Fit side-chains REVERT: A 393 MET cc_start: 0.8180 (ttp) cc_final: 0.7883 (ttm) REVERT: A 445 LYS cc_start: 0.7702 (pttp) cc_final: 0.7078 (pptt) REVERT: A 461 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7943 (t80) REVERT: A 490 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6722 (tm-30) REVERT: A 515 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8486 (mtm) REVERT: A 734 MET cc_start: 0.8429 (tpp) cc_final: 0.7888 (tpp) REVERT: B 376 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8178 (tp) REVERT: B 461 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.7828 (t80) REVERT: B 583 MET cc_start: 0.8288 (tpp) cc_final: 0.7928 (mmm) outliers start: 24 outliers final: 17 residues processed: 189 average time/residue: 0.1033 time to fit residues: 28.9519 Evaluate side-chains 187 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 226 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 VAL 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 448 LEU Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET 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 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 544 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 144 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.130189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.111366 restraints weight = 15594.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.110130 restraints weight = 29925.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107621 restraints weight = 23911.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.108299 restraints weight = 24507.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.107478 restraints weight = 18357.476| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 12237 Z= 0.114 Angle : 0.627 10.602 16748 Z= 0.296 Chirality : 0.040 0.156 1774 Planarity : 0.004 0.046 2077 Dihedral : 6.601 76.659 1636 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.16 % Allowed : 17.63 % 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: -1.59 (0.22), residues: 1468 helix: -0.35 (0.18), residues: 894 sheet: None (None), residues: 0 loop : -2.14 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 168 TYR 0.025 0.001 TYR B 362 PHE 0.031 0.001 PHE A 503 TRP 0.035 0.001 TRP B 426 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00289 (12233) covalent geometry : angle 0.62676 (16748) hydrogen bonds : bond 0.03413 ( 460) hydrogen bonds : angle 3.86884 ( 1329) Misc. bond : bond 0.06560 ( 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 196 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.423 Fit side-chains REVERT: A 168 ARG cc_start: 0.6885 (tpp80) cc_final: 0.6556 (mtm110) REVERT: A 177 GLU cc_start: 0.7466 (tp30) cc_final: 0.6962 (pp20) REVERT: A 425 PHE cc_start: 0.8637 (t80) cc_final: 0.8075 (t80) REVERT: A 445 LYS cc_start: 0.7829 (pttp) cc_final: 0.7132 (pptt) REVERT: A 461 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.7915 (t80) REVERT: A 490 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6703 (tm-30) REVERT: A 515 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8532 (mtm) REVERT: A 734 MET cc_start: 0.8286 (tpp) cc_final: 0.7712 (tpp) REVERT: B 298 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8253 (mm) REVERT: B 376 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8094 (tp) REVERT: B 425 PHE cc_start: 0.8627 (t80) cc_final: 0.7987 (t80) REVERT: B 461 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.7949 (t80) REVERT: B 555 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7932 (t80) REVERT: B 583 MET cc_start: 0.8359 (tpp) cc_final: 0.8009 (mmm) outliers start: 25 outliers final: 15 residues processed: 184 average time/residue: 0.1027 time to fit residues: 28.0449 Evaluate side-chains 191 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 348 LEU 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 478 GLU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 196 THR 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 461 PHE 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 106 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.130263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.111669 restraints weight = 15853.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.111678 restraints weight = 29285.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.109900 restraints weight = 19243.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.110698 restraints weight = 22914.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.110360 restraints weight = 16997.060| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 12237 Z= 0.131 Angle : 0.646 10.861 16748 Z= 0.305 Chirality : 0.042 0.153 1774 Planarity : 0.004 0.046 2077 Dihedral : 6.637 76.582 1636 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.07 % Allowed : 17.72 % 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: -1.56 (0.22), residues: 1468 helix: -0.32 (0.18), residues: 892 sheet: None (None), residues: 0 loop : -2.13 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.016 0.001 TYR B 324 PHE 0.029 0.001 PHE A 503 TRP 0.035 0.001 TRP B 426 HIS 0.006 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00334 (12233) covalent geometry : angle 0.64591 (16748) hydrogen bonds : bond 0.03586 ( 460) hydrogen bonds : angle 3.92390 ( 1329) Misc. bond : bond 0.07985 ( 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 194 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.414 Fit side-chains REVERT: A 168 ARG cc_start: 0.6837 (tpp80) cc_final: 0.6515 (mtm110) REVERT: A 445 LYS cc_start: 0.7622 (pttp) cc_final: 0.7047 (pptt) REVERT: A 461 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.7992 (t80) REVERT: A 490 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6802 (tm-30) REVERT: A 515 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8431 (mtm) REVERT: A 734 MET cc_start: 0.8319 (tpp) cc_final: 0.7745 (tpp) REVERT: B 287 PHE cc_start: 0.8423 (t80) cc_final: 0.8035 (t80) REVERT: B 298 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8258 (mm) REVERT: B 376 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8061 (tp) REVERT: B 461 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.7983 (t80) REVERT: B 555 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7934 (t80) outliers start: 24 outliers final: 16 residues processed: 184 average time/residue: 0.0991 time to fit residues: 27.0773 Evaluate side-chains 187 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 348 LEU 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 478 GLU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 196 THR 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 461 PHE Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 695 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 119 optimal weight: 0.6980 chunk 111 optimal weight: 0.0670 chunk 110 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.136630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.119145 restraints weight = 15443.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.119007 restraints weight = 28496.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.116686 restraints weight = 21617.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.117935 restraints weight = 22721.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.117273 restraints weight = 17621.199| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 12237 Z= 0.112 Angle : 0.630 10.111 16748 Z= 0.297 Chirality : 0.040 0.235 1774 Planarity : 0.004 0.046 2077 Dihedral : 6.542 77.227 1636 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.82 % Allowed : 18.32 % 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: -1.41 (0.22), residues: 1468 helix: -0.20 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.05 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 90 TYR 0.023 0.001 TYR A 362 PHE 0.029 0.001 PHE A 503 TRP 0.034 0.001 TRP A 426 HIS 0.004 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00283 (12233) covalent geometry : angle 0.62993 (16748) hydrogen bonds : bond 0.03336 ( 460) hydrogen bonds : angle 3.85426 ( 1329) Misc. bond : bond 0.06217 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1599.60 seconds wall clock time: 28 minutes 29.84 seconds (1709.84 seconds total)