Starting phenix.real_space_refine on Wed Jul 30 02:44:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qq5_4618/07_2025/6qq5_4618.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qq5_4618/07_2025/6qq5_4618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qq5_4618/07_2025/6qq5_4618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qq5_4618/07_2025/6qq5_4618.map" model { file = "/net/cci-nas-00/data/ceres_data/6qq5_4618/07_2025/6qq5_4618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qq5_4618/07_2025/6qq5_4618.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.86, per 1000 atoms: 0.58 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: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.07 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: 2.87 Time building geometry restraints manager: 3.18 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 743 or resid 801 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: 0.620 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.520 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.840 ------------------------------------------------------------------------------- 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 : 4.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.002 TRP A 338 HIS 0.011 0.002 HIS B 537 PHE 0.023 0.002 PHE A 635 TYR 0.019 0.002 TYR B 618 ARG 0.006 0.001 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.24132 ( 460) hydrogen bonds : angle 8.27031 ( 1329) covalent geometry : bond 0.00709 (12233) covalent geometry : angle 1.07086 (16748) 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 : 1.139 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: 0.8246 (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: 0.8019 (mtp) REVERT: A 445 LYS cc_start: 0.7814 (pttp) cc_final: 0.7570 (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: 0.8430 (t80) REVERT: A 583 MET cc_start: 0.8871 (tpp) cc_final: 0.8593 (tpp) REVERT: A 584 GLU cc_start: 0.8180 (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: 0.8002 (mmt) cc_final: 0.7699 (mmt) REVERT: B 186 ARG cc_start: 0.8161 (ptt-90) cc_final: 0.7784 (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: 0.8552 (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: 0.8967 (m-10) REVERT: B 734 MET cc_start: 0.8699 (tpp) cc_final: 0.7929 (tpp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2763 time to fit residues: 92.6532 Evaluate side-chains 204 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 305 HIS B 385 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.129695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.110040 restraints weight = 15605.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.109845 restraints weight = 31618.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.107201 restraints weight = 23121.202| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 12237 Z= 0.136 Angle : 0.690 13.198 16748 Z= 0.335 Chirality : 0.041 0.153 1774 Planarity : 0.005 0.055 2077 Dihedral : 7.467 75.489 1636 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.18), residues: 1468 helix: -2.57 (0.14), residues: 910 sheet: None (None), residues: 0 loop : -3.07 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 338 HIS 0.005 0.001 HIS B 537 PHE 0.013 0.001 PHE B 503 TYR 0.017 0.001 TYR B 406 ARG 0.008 0.001 ARG B 513 Details of bonding type rmsd hydrogen bonds : bond 0.04943 ( 460) hydrogen bonds : angle 4.84664 ( 1329) covalent geometry : bond 0.00321 (12233) covalent geometry : angle 0.68966 (16748) Misc. bond : bond 0.13032 ( 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 230 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 182 ASP cc_start: 0.7572 (t70) cc_final: 0.6939 (m-30) REVERT: A 296 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8197 (tm-30) REVERT: A 376 LEU cc_start: 0.8388 (tt) cc_final: 0.7839 (tp) REVERT: A 393 MET cc_start: 0.8153 (ttm) cc_final: 0.7719 (ttm) REVERT: A 445 LYS cc_start: 0.7728 (pttp) cc_final: 0.7469 (pptt) REVERT: A 490 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6669 (tm-30) REVERT: A 584 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 734 MET cc_start: 0.8504 (tpp) cc_final: 0.7892 (tpp) REVERT: B 425 PHE cc_start: 0.8668 (t80) cc_final: 0.8121 (t80) REVERT: B 490 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7068 (tm-30) REVERT: B 569 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7615 (tt0) outliers start: 16 outliers final: 10 residues processed: 218 average time/residue: 0.2846 time to fit residues: 89.8342 Evaluate side-chains 199 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 34 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 191 HIS A 473 HIS B 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.132791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.114180 restraints weight = 15717.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.114314 restraints weight = 30065.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.112993 restraints weight = 20719.166| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 12237 Z= 0.166 Angle : 0.684 14.292 16748 Z= 0.326 Chirality : 0.042 0.150 1774 Planarity : 0.004 0.052 2077 Dihedral : 7.218 72.548 1636 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 1.73 % Allowed : 13.05 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.20), residues: 1468 helix: -1.82 (0.16), residues: 908 sheet: None (None), residues: 0 loop : -2.83 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 338 HIS 0.019 0.002 HIS A 191 PHE 0.021 0.001 PHE A 503 TYR 0.026 0.001 TYR B 362 ARG 0.004 0.000 ARG B 513 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 460) hydrogen bonds : angle 4.53064 ( 1329) covalent geometry : bond 0.00413 (12233) covalent geometry : angle 0.68417 (16748) Misc. bond : bond 0.12545 ( 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: 20 poor density : 192 time to evaluate : 1.227 Fit side-chains REVERT: A 393 MET cc_start: 0.8063 (ttm) cc_final: 0.7681 (ttm) REVERT: A 445 LYS cc_start: 0.7689 (pttp) cc_final: 0.7434 (pptt) REVERT: A 490 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6693 (tm-30) REVERT: A 555 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7994 (t80) REVERT: A 734 MET cc_start: 0.8517 (tpp) cc_final: 0.7917 (tpp) REVERT: B 31 ARG cc_start: 0.7964 (ptt180) cc_final: 0.7729 (ptt180) REVERT: B 296 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8439 (tm-30) REVERT: B 425 PHE cc_start: 0.8671 (t80) cc_final: 0.8076 (t80) REVERT: B 490 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7172 (tm-30) REVERT: B 569 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7642 (tt0) REVERT: B 734 MET cc_start: 0.8562 (tpp) cc_final: 0.8110 (tpp) outliers start: 20 outliers final: 15 residues processed: 203 average time/residue: 0.2820 time to fit residues: 85.1321 Evaluate side-chains 200 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 389 ILE 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 555 PHE Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS 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 = 0.3325 r_free = 0.3325 target = 0.127862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.109841 restraints weight = 15941.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.109312 restraints weight = 30777.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.106968 restraints weight = 22416.294| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 12237 Z= 0.125 Angle : 0.632 13.249 16748 Z= 0.301 Chirality : 0.040 0.145 1774 Planarity : 0.004 0.050 2077 Dihedral : 6.943 75.401 1636 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.16 % Allowed : 14.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.21), residues: 1468 helix: -1.34 (0.17), residues: 906 sheet: None (None), residues: 0 loop : -2.69 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 426 HIS 0.006 0.001 HIS B 191 PHE 0.026 0.001 PHE A 503 TYR 0.012 0.001 TYR B 324 ARG 0.007 0.000 ARG A 513 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 460) hydrogen bonds : angle 4.24828 ( 1329) covalent geometry : bond 0.00314 (12233) covalent geometry : angle 0.63194 (16748) Misc. bond : bond 0.09228 ( 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 219 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 393 MET cc_start: 0.8003 (ttm) cc_final: 0.7604 (ttm) REVERT: A 445 LYS cc_start: 0.7645 (pttp) cc_final: 0.7295 (pptt) REVERT: A 490 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6739 (tm-30) REVERT: A 555 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7962 (t80) REVERT: A 734 MET cc_start: 0.8435 (tpp) cc_final: 0.7830 (tpp) REVERT: B 31 ARG cc_start: 0.7920 (ptt180) cc_final: 0.7660 (ptt180) REVERT: B 296 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8450 (tm-30) REVERT: B 734 MET cc_start: 0.8452 (tpp) cc_final: 0.7965 (tpp) outliers start: 25 outliers final: 17 residues processed: 206 average time/residue: 0.2738 time to fit residues: 82.1414 Evaluate side-chains 201 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 226 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 290 VAL 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 26 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 131 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 473 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.126140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.108423 restraints weight = 16060.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107619 restraints weight = 31675.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.104960 restraints weight = 26311.837| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 12237 Z= 0.161 Angle : 0.652 13.082 16748 Z= 0.310 Chirality : 0.042 0.148 1774 Planarity : 0.004 0.048 2077 Dihedral : 6.956 73.875 1636 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.51 % Allowed : 15.90 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.21), residues: 1468 helix: -1.10 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -2.52 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 426 HIS 0.007 0.001 HIS B 537 PHE 0.014 0.001 PHE B 593 TYR 0.028 0.001 TYR B 362 ARG 0.003 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 460) hydrogen bonds : angle 4.19699 ( 1329) covalent geometry : bond 0.00407 (12233) covalent geometry : angle 0.65158 (16748) Misc. bond : bond 0.10808 ( 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 213 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 1.301 Fit side-chains REVERT: A 393 MET cc_start: 0.8008 (ttm) cc_final: 0.7628 (ttm) REVERT: A 445 LYS cc_start: 0.7709 (pttp) cc_final: 0.7249 (pptt) REVERT: A 490 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6764 (tm-30) REVERT: A 555 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8131 (t80) REVERT: A 734 MET cc_start: 0.8460 (tpp) cc_final: 0.7856 (tpp) REVERT: B 31 ARG cc_start: 0.7901 (ptt180) cc_final: 0.7615 (ptt180) REVERT: B 296 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8452 (tm-30) REVERT: B 490 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7115 (tm-30) REVERT: B 734 MET cc_start: 0.8434 (tpp) cc_final: 0.7958 (tpp) outliers start: 29 outliers final: 17 residues processed: 202 average time/residue: 0.2235 time to fit residues: 66.8090 Evaluate side-chains 197 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 SER 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 104 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 133 optimal weight: 0.4980 chunk 125 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 115 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS B 331 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.135333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.118285 restraints weight = 15586.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.118163 restraints weight = 28314.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.116050 restraints weight = 19718.798| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2368 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= 0.112 Angle : 0.621 11.137 16748 Z= 0.296 Chirality : 0.040 0.142 1774 Planarity : 0.004 0.048 2077 Dihedral : 6.756 76.410 1636 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.99 % Allowed : 16.85 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.22), residues: 1468 helix: -0.77 (0.18), residues: 882 sheet: None (None), residues: 0 loop : -2.38 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 426 HIS 0.005 0.001 HIS B 537 PHE 0.017 0.001 PHE B 503 TYR 0.019 0.001 TYR B 324 ARG 0.004 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 460) hydrogen bonds : angle 3.98660 ( 1329) covalent geometry : bond 0.00282 (12233) covalent geometry : angle 0.62064 (16748) Misc. bond : bond 0.07294 ( 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 201 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.245 Fit side-chains REVERT: A 376 LEU cc_start: 0.8340 (tp) cc_final: 0.7840 (tp) REVERT: A 393 MET cc_start: 0.7973 (ttm) cc_final: 0.7572 (ttm) REVERT: A 445 LYS cc_start: 0.7674 (pttp) cc_final: 0.7195 (pptt) REVERT: A 490 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6766 (tm-30) REVERT: A 529 LEU cc_start: 0.9004 (tp) cc_final: 0.8753 (tp) REVERT: A 555 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7968 (t80) REVERT: A 734 MET cc_start: 0.8423 (tpp) cc_final: 0.7829 (tpp) REVERT: B 31 ARG cc_start: 0.7902 (ptt180) cc_final: 0.7613 (ptt180) REVERT: B 376 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8089 (tp) REVERT: B 425 PHE cc_start: 0.8639 (t80) cc_final: 0.8028 (t80) REVERT: B 461 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.7796 (t80) outliers start: 23 outliers final: 15 residues processed: 192 average time/residue: 0.2211 time to fit residues: 62.8785 Evaluate side-chains 191 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 387 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 23 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 331 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.133922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.116421 restraints weight = 15777.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116992 restraints weight = 28472.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.114174 restraints weight = 21733.343| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 12237 Z= 0.137 Angle : 0.635 13.649 16748 Z= 0.299 Chirality : 0.041 0.146 1774 Planarity : 0.004 0.047 2077 Dihedral : 6.774 75.221 1636 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.77 % Allowed : 17.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.22), residues: 1468 helix: -0.63 (0.18), residues: 882 sheet: None (None), residues: 0 loop : -2.28 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 426 HIS 0.006 0.001 HIS A 537 PHE 0.014 0.001 PHE A 24 TYR 0.026 0.001 TYR B 362 ARG 0.002 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 460) hydrogen bonds : angle 3.99510 ( 1329) covalent geometry : bond 0.00351 (12233) covalent geometry : angle 0.63503 (16748) Misc. bond : bond 0.10057 ( 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 207 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 1.322 Fit side-chains REVERT: A 376 LEU cc_start: 0.8385 (tp) cc_final: 0.7896 (tp) REVERT: A 393 MET cc_start: 0.7951 (ttm) cc_final: 0.7590 (ttm) REVERT: A 425 PHE cc_start: 0.8623 (t80) cc_final: 0.8119 (t80) REVERT: A 445 LYS cc_start: 0.7717 (pttp) cc_final: 0.7242 (pptt) REVERT: A 490 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6801 (tm-30) REVERT: A 515 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8338 (mtm) REVERT: A 529 LEU cc_start: 0.9042 (tp) cc_final: 0.8778 (tp) REVERT: A 555 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 734 MET cc_start: 0.8428 (tpp) cc_final: 0.7833 (tpp) REVERT: B 31 ARG cc_start: 0.7902 (ptt180) cc_final: 0.7616 (ptt180) REVERT: B 348 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8121 (tt) REVERT: B 376 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8543 (tp) REVERT: B 425 PHE cc_start: 0.8652 (t80) cc_final: 0.8067 (t80) REVERT: B 461 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.7864 (t80) outliers start: 32 outliers final: 20 residues processed: 195 average time/residue: 0.2238 time to fit residues: 64.8007 Evaluate side-chains 194 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 325 SER Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 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 489 VAL Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 695 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 126 optimal weight: 3.9990 chunk 143 optimal weight: 0.0370 chunk 132 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 84 optimal weight: 0.0070 chunk 140 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.130789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.112027 restraints weight = 15796.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.111759 restraints weight = 29752.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.109421 restraints weight = 19962.837| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12237 Z= 0.106 Angle : 0.611 10.892 16748 Z= 0.290 Chirality : 0.040 0.320 1774 Planarity : 0.004 0.047 2077 Dihedral : 6.600 77.409 1636 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.82 % Allowed : 18.24 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.22), residues: 1468 helix: -0.41 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -2.21 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 426 HIS 0.004 0.001 HIS B 537 PHE 0.023 0.001 PHE A 503 TYR 0.020 0.001 TYR B 324 ARG 0.005 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 460) hydrogen bonds : angle 3.85214 ( 1329) covalent geometry : bond 0.00266 (12233) covalent geometry : angle 0.61062 (16748) Misc. bond : bond 0.06097 ( 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 206 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.202 Fit side-chains REVERT: A 168 ARG cc_start: 0.6798 (tpp80) cc_final: 0.6544 (mtm110) REVERT: A 376 LEU cc_start: 0.8382 (tp) cc_final: 0.7890 (tp) REVERT: A 393 MET cc_start: 0.8006 (ttm) cc_final: 0.7630 (ttm) REVERT: A 425 PHE cc_start: 0.8625 (t80) cc_final: 0.8043 (t80) REVERT: A 445 LYS cc_start: 0.7699 (pttp) cc_final: 0.7129 (pptt) REVERT: A 461 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7928 (t80) REVERT: A 490 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6740 (tm-30) REVERT: A 515 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8412 (mtm) REVERT: A 734 MET cc_start: 0.8369 (tpp) cc_final: 0.7812 (tpp) REVERT: B 376 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8114 (tp) REVERT: B 461 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.7901 (t80) REVERT: B 602 LEU cc_start: 0.8947 (tp) cc_final: 0.8709 (tp) outliers start: 21 outliers final: 15 residues processed: 197 average time/residue: 0.2250 time to fit residues: 65.5485 Evaluate side-chains 191 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 348 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 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 54 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.127985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.110061 restraints weight = 16067.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109402 restraints weight = 30818.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.107355 restraints weight = 20818.609| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 12237 Z= 0.148 Angle : 0.648 11.950 16748 Z= 0.306 Chirality : 0.042 0.277 1774 Planarity : 0.004 0.046 2077 Dihedral : 6.704 75.700 1636 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.07 % Allowed : 18.32 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.22), residues: 1468 helix: -0.37 (0.18), residues: 882 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 426 HIS 0.006 0.001 HIS A 537 PHE 0.011 0.001 PHE A 503 TYR 0.019 0.001 TYR B 324 ARG 0.004 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 460) hydrogen bonds : angle 3.99872 ( 1329) covalent geometry : bond 0.00381 (12233) covalent geometry : angle 0.64756 (16748) Misc. bond : bond 0.09026 ( 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: 24 poor density : 172 time to evaluate : 1.258 Fit side-chains REVERT: A 376 LEU cc_start: 0.8386 (tp) cc_final: 0.7896 (tp) REVERT: A 393 MET cc_start: 0.7945 (ttm) cc_final: 0.7589 (ttm) REVERT: A 425 PHE cc_start: 0.8656 (t80) cc_final: 0.8167 (t80) REVERT: A 445 LYS cc_start: 0.7779 (pttp) cc_final: 0.7175 (pptt) REVERT: A 490 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6758 (tm-30) REVERT: A 515 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8449 (mtm) REVERT: A 734 MET cc_start: 0.8299 (tpp) cc_final: 0.7725 (tpp) REVERT: B 287 PHE cc_start: 0.8439 (t80) cc_final: 0.8075 (t80) REVERT: B 344 LEU cc_start: 0.8558 (mt) cc_final: 0.8105 (mt) REVERT: B 376 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8548 (tp) REVERT: B 461 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.7884 (t80) outliers start: 24 outliers final: 17 residues processed: 188 average time/residue: 0.2417 time to fit residues: 66.4865 Evaluate side-chains 187 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 348 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 110 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 20 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.129297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.111423 restraints weight = 15900.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.110770 restraints weight = 30682.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.108543 restraints weight = 20663.443| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 12237 Z= 0.123 Angle : 0.630 11.166 16748 Z= 0.298 Chirality : 0.041 0.277 1774 Planarity : 0.004 0.046 2077 Dihedral : 6.638 76.872 1636 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.07 % Allowed : 18.32 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1468 helix: -0.26 (0.18), residues: 882 sheet: None (None), residues: 0 loop : -2.11 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 426 HIS 0.005 0.001 HIS A 537 PHE 0.029 0.001 PHE A 503 TYR 0.025 0.001 TYR A 657 ARG 0.005 0.000 ARG B 267 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 460) hydrogen bonds : angle 3.93687 ( 1329) covalent geometry : bond 0.00316 (12233) covalent geometry : angle 0.63044 (16748) Misc. bond : bond 0.07864 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 1.231 Fit side-chains REVERT: A 376 LEU cc_start: 0.8367 (tp) cc_final: 0.7859 (tp) REVERT: A 425 PHE cc_start: 0.8598 (t80) cc_final: 0.8131 (t80) REVERT: A 445 LYS cc_start: 0.7698 (pttp) cc_final: 0.7125 (pptt) REVERT: A 461 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7987 (t80) REVERT: A 515 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8450 (mtm) REVERT: A 555 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7899 (t80) REVERT: A 734 MET cc_start: 0.8342 (tpp) cc_final: 0.7767 (tpp) REVERT: B 287 PHE cc_start: 0.8422 (t80) cc_final: 0.8049 (t80) REVERT: B 344 LEU cc_start: 0.8503 (mt) cc_final: 0.8239 (mt) REVERT: B 376 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8089 (tp) REVERT: B 425 PHE cc_start: 0.8633 (t80) cc_final: 0.8067 (t80) REVERT: B 461 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.7978 (t80) outliers start: 24 outliers final: 17 residues processed: 187 average time/residue: 0.2217 time to fit residues: 60.6904 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 : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.134909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.117153 restraints weight = 15558.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.116503 restraints weight = 28597.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.113365 restraints weight = 23882.434| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 12237 Z= 0.121 Angle : 0.638 10.809 16748 Z= 0.302 Chirality : 0.041 0.279 1774 Planarity : 0.004 0.046 2077 Dihedral : 6.610 77.384 1636 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.99 % Allowed : 18.58 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.23), residues: 1468 helix: -0.18 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -2.08 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 426 HIS 0.005 0.001 HIS B 537 PHE 0.029 0.001 PHE A 503 TYR 0.018 0.001 TYR B 324 ARG 0.005 0.000 ARG B 267 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 460) hydrogen bonds : angle 3.90369 ( 1329) covalent geometry : bond 0.00309 (12233) covalent geometry : angle 0.63831 (16748) Misc. bond : bond 0.07343 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3299.97 seconds wall clock time: 59 minutes 23.77 seconds (3563.77 seconds total)