Starting phenix.real_space_refine on Fri Jul 3 22:25:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7shf_25126/07_2026/7shf_25126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7shf_25126/07_2026/7shf_25126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7shf_25126/07_2026/7shf_25126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7shf_25126/07_2026/7shf_25126.map" model { file = "/net/cci-nas-00/data/ceres_data/7shf_25126/07_2026/7shf_25126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7shf_25126/07_2026/7shf_25126.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7shf_25126/07_2026/7shf_25126.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7shf_25126/07_2026/7shf_25126.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5953 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 67 5.16 5 C 7608 2.51 5 N 1808 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11443 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3329 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3318 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 374} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 400, 3318 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 374} Chain breaks: 1 bond proxies already assigned to first conformer: 3394 Chain: "D" Number of atoms: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2660 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 339} Chain: "B" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2322 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2412 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 280 Unusual residues: {'CLR': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 440 Unusual residues: {'CLR': 12, 'EIJ': 1, 'PEE': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG C 271 " occ=0.46 ... (20 atoms not shown) pdb=" NH2BARG C 271 " occ=0.54 Time building chain proxies: 2.42, per 1000 atoms: 0.21 Number of scatterers: 11443 At special positions: 0 Unit cell: (79.443, 109.125, 184.203, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 2 15.00 O 1958 8.00 N 1808 7.00 C 7608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 481 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 481 " - pdb=" SG CYS A 573 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 614.6 milliseconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 10 sheets defined 50.4% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 20 through 35 removed outlier: 3.659A pdb=" N LYS C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 removed outlier: 3.739A pdb=" N VAL C 63 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.631A pdb=" N CYS C 120 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 138 removed outlier: 3.528A pdb=" N TYR C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA C 129 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 160 removed outlier: 3.523A pdb=" N GLU C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 180 removed outlier: 3.628A pdb=" N LYS C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 removed outlier: 3.634A pdb=" N ASP C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 254 through 271 removed outlier: 4.058A pdb=" N LEU C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN C 268 " --> pdb=" O TYR C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 290 removed outlier: 3.587A pdb=" N TYR C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.719A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 removed outlier: 3.871A pdb=" N GLY C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 removed outlier: 3.529A pdb=" N ASP C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 355 Processing helix chain 'C' and resid 357 through 371 removed outlier: 3.601A pdb=" N VAL C 366 " --> pdb=" O PHE C 362 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU C 367 " --> pdb=" O TRP C 363 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 376 through 389 removed outlier: 3.879A pdb=" N GLN C 382 " --> pdb=" O PRO C 378 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 389 " --> pdb=" O TRP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 411 Processing helix chain 'C' and resid 419 through 433 removed outlier: 3.575A pdb=" N LEU C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 Processing helix chain 'C' and resid 441 through 449 removed outlier: 3.862A pdb=" N GLN C 445 " --> pdb=" O SER C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 34 Processing helix chain 'D' and resid 37 through 43 Processing helix chain 'D' and resid 141 through 146 removed outlier: 4.136A pdb=" N LYS D 145 " --> pdb=" O ASN D 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 442 removed outlier: 3.777A pdb=" N ILE B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 432 " --> pdb=" O MET B 428 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR B 439 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 451 removed outlier: 3.975A pdb=" N SER B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 457 Processing helix chain 'B' and resid 457 through 465 removed outlier: 4.609A pdb=" N LEU B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 removed outlier: 3.923A pdb=" N VAL B 470 " --> pdb=" O TYR B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 removed outlier: 3.556A pdb=" N PHE B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 504 through 509 removed outlier: 3.568A pdb=" N VAL B 509 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 removed outlier: 3.882A pdb=" N THR B 514 " --> pdb=" O PHE B 510 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 515' Processing helix chain 'B' and resid 532 through 546 removed outlier: 3.593A pdb=" N VAL B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.784A pdb=" N ASN B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.901A pdb=" N MET B 581 " --> pdb=" O ARG B 577 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 584 " --> pdb=" O TYR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 599 removed outlier: 3.786A pdb=" N GLY B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 622 through 634 removed outlier: 3.575A pdb=" N PHE B 627 " --> pdb=" O ILE B 623 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 652 removed outlier: 3.519A pdb=" N LEU B 646 " --> pdb=" O TRP B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 662 removed outlier: 3.619A pdb=" N THR B 658 " --> pdb=" O THR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 730 removed outlier: 3.776A pdb=" N LYS B 719 " --> pdb=" O ARG B 715 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 720 " --> pdb=" O ASP B 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.607A pdb=" N ILE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.644A pdb=" N CYS A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 442 removed outlier: 3.575A pdb=" N HIS A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 466 through 475 removed outlier: 4.089A pdb=" N VAL A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 472 " --> pdb=" O PRO A 468 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.538A pdb=" N ALA A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.859A pdb=" N LYS A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 548 removed outlier: 3.813A pdb=" N ILE A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 555 removed outlier: 4.011A pdb=" N LYS A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 550 through 555' Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.572A pdb=" N PHE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 596 removed outlier: 3.773A pdb=" N GLY A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 614 through 634 removed outlier: 3.504A pdb=" N HIS A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 622 " --> pdb=" O HIS A 618 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 627 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 709 through 731 removed outlier: 3.849A pdb=" N ILE A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG A 715 " --> pdb=" O PRO A 711 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 719 " --> pdb=" O ARG A 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 726 " --> pdb=" O TYR A 722 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS A 731 " --> pdb=" O ILE A 727 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 47 removed outlier: 5.908A pdb=" N ARG C 44 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 11.255A pdb=" N SER C 55 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE C 110 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 54 through 59 removed outlier: 6.708A pdb=" N VAL D 351 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR D 58 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU D 349 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG D 350 " --> pdb=" O SER D 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 66 through 71 removed outlier: 3.813A pdb=" N CYS D 68 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 78 " --> pdb=" O TRP D 90 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASP D 91 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS D 97 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 110 through 113 removed outlier: 6.405A pdb=" N CYS D 129 " --> pdb=" O VAL D 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 156 through 161 removed outlier: 6.889A pdb=" N ALA D 171 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N CYS D 159 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU D 169 " --> pdb=" O CYS D 159 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE D 161 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLN D 167 " --> pdb=" O PHE D 161 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 189 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP D 181 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU D 187 " --> pdb=" O ASP D 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 198 through 203 removed outlier: 3.774A pdb=" N PHE D 212 " --> pdb=" O TRP D 224 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 223 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D 233 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 242 through 247 removed outlier: 3.748A pdb=" N PHE D 254 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA D 275 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 286 through 291 removed outlier: 3.688A pdb=" N SER D 288 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER D 319 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASP D 311 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG D 317 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 562 through 563 Processing sheet with id=AB1, first strand: chain 'A' and resid 559 through 563 399 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1698 1.30 - 1.43: 3042 1.43 - 1.56: 6883 1.56 - 1.68: 38 1.68 - 1.81: 106 Bond restraints: 11767 Sorted by residual: bond pdb=" C09 EIJ A 813 " pdb=" C10 EIJ A 813 " ideal model delta sigma weight residual 1.330 1.547 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C12 EIJ A 813 " pdb=" C13 EIJ A 813 " ideal model delta sigma weight residual 1.330 1.541 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C06 EIJ A 813 " pdb=" C07 EIJ A 813 " ideal model delta sigma weight residual 1.330 1.539 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C24 PEE A 814 " pdb=" C25 PEE A 814 " ideal model delta sigma weight residual 1.523 1.319 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C03 EIJ A 813 " pdb=" C04 EIJ A 813 " ideal model delta sigma weight residual 1.330 1.533 -0.203 2.00e-02 2.50e+03 1.03e+02 ... (remaining 11762 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.42: 16026 8.42 - 16.84: 17 16.84 - 25.26: 1 25.26 - 33.68: 0 33.68 - 42.10: 3 Bond angle restraints: 16047 Sorted by residual: angle pdb=" C07 EIJ A 813 " pdb=" C08 EIJ A 813 " pdb=" C09 EIJ A 813 " ideal model delta sigma weight residual 111.63 153.73 -42.10 3.00e+00 1.11e-01 1.97e+02 angle pdb=" C21 PEE A 814 " pdb=" C22 PEE A 814 " pdb=" C23 PEE A 814 " ideal model delta sigma weight residual 113.44 152.74 -39.30 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C18 PEE A 814 " pdb=" C19 PEE A 814 " pdb=" C20 PEE A 814 " ideal model delta sigma weight residual 113.02 152.27 -39.25 3.00e+00 1.11e-01 1.71e+02 angle pdb=" N PRO C 299 " pdb=" CA PRO C 299 " pdb=" C PRO C 299 " ideal model delta sigma weight residual 110.70 122.62 -11.92 1.22e+00 6.72e-01 9.55e+01 angle pdb=" N PRO A 407 " pdb=" CA PRO A 407 " pdb=" CB PRO A 407 " ideal model delta sigma weight residual 103.25 111.32 -8.07 1.05e+00 9.07e-01 5.90e+01 ... (remaining 16042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 6579 32.98 - 65.97: 234 65.97 - 98.95: 23 98.95 - 131.93: 13 131.93 - 164.92: 2 Dihedral angle restraints: 6851 sinusoidal: 2943 harmonic: 3908 Sorted by residual: dihedral pdb=" CB CYS A 481 " pdb=" SG CYS A 481 " pdb=" SG CYS A 573 " pdb=" CB CYS A 573 " ideal model delta sinusoidal sigma weight residual 93.00 168.86 -75.86 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS B 481 " pdb=" SG CYS B 481 " pdb=" SG CYS B 573 " pdb=" CB CYS B 573 " ideal model delta sinusoidal sigma weight residual 93.00 167.20 -74.20 1 1.00e+01 1.00e-02 6.99e+01 dihedral pdb=" C36 PEE A 814 " pdb=" C37 PEE A 814 " pdb=" C38 PEE A 814 " pdb=" C39 PEE A 814 " ideal model delta sinusoidal sigma weight residual -179.40 -14.48 -164.92 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 6848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.009: 1839 1.009 - 2.018: 0 2.018 - 3.027: 0 3.027 - 4.036: 0 4.036 - 5.045: 8 Chirality restraints: 1847 Sorted by residual: chirality pdb=" C17 CLR A 809 " pdb=" C13 CLR A 809 " pdb=" C16 CLR A 809 " pdb=" C20 CLR A 809 " both_signs ideal model delta sigma weight residual False 2.55 -2.49 5.05 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" C17 CLR A 804 " pdb=" C13 CLR A 804 " pdb=" C16 CLR A 804 " pdb=" C20 CLR A 804 " both_signs ideal model delta sigma weight residual False 2.55 -2.43 4.98 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" C47 EIJ A 813 " pdb=" C46 EIJ A 813 " pdb=" C49 EIJ A 813 " pdb=" O48 EIJ A 813 " both_signs ideal model delta sigma weight residual False 2.41 -2.53 4.94 2.00e-01 2.50e+01 6.10e+02 ... (remaining 1844 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 EIJ A 813 " 0.164 2.00e-02 2.50e+03 3.36e-01 1.13e+03 pdb=" C12 EIJ A 813 " -0.454 2.00e-02 2.50e+03 pdb=" C13 EIJ A 813 " 0.442 2.00e-02 2.50e+03 pdb=" C14 EIJ A 813 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 EIJ A 813 " -0.103 2.00e-02 2.50e+03 1.03e-01 1.05e+02 pdb=" C03 EIJ A 813 " 0.105 2.00e-02 2.50e+03 pdb=" C04 EIJ A 813 " 0.100 2.00e-02 2.50e+03 pdb=" C05 EIJ A 813 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 EIJ A 813 " -0.070 2.00e-02 2.50e+03 6.43e-02 4.13e+01 pdb=" C06 EIJ A 813 " 0.076 2.00e-02 2.50e+03 pdb=" C07 EIJ A 813 " 0.050 2.00e-02 2.50e+03 pdb=" C08 EIJ A 813 " -0.057 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 751 2.73 - 3.27: 11100 3.27 - 3.82: 16864 3.82 - 4.36: 22090 4.36 - 4.90: 36809 Nonbonded interactions: 87614 Sorted by model distance: nonbonded pdb=" OD1 ASP D 346 " pdb=" OG1 THR D 348 " model vdw 2.190 3.040 nonbonded pdb=" OD1 ASP D 304 " pdb=" OG1 THR D 306 " model vdw 2.198 3.040 nonbonded pdb=" O ARG A 715 " pdb=" NZ LYS A 719 " model vdw 2.245 3.120 nonbonded pdb=" O CYS A 481 " pdb=" NH1 ARG A 485 " model vdw 2.250 3.120 nonbonded pdb=" CE2 PHE B 460 " pdb=" C23 CLR B 803 " model vdw 2.258 3.740 ... (remaining 87609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 406 through 670 or resid 712 through 730 or resid 805 thro \ ugh 812)) selection = (chain 'B' and ((resid 406 through 408 and (name N or name CA or name C or name \ O or name CB )) or resid 409 through 808)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.430 11770 Z= 0.562 Angle : 1.047 42.098 16051 Z= 0.494 Chirality : 0.324 5.045 1847 Planarity : 0.010 0.336 1862 Dihedral : 17.515 164.917 4309 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.09 % Favored : 92.38 % Rotamer: Outliers : 0.68 % Allowed : 0.43 % Favored : 98.89 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.22), residues: 1315 helix: -2.50 (0.18), residues: 665 sheet: -0.78 (0.45), residues: 137 loop : -1.42 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 109 TYR 0.044 0.002 TYR A 496 PHE 0.034 0.002 PHE A 474 TRP 0.039 0.002 TRP C 65 HIS 0.006 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00805 / 0.40 (11767) covalent geometry : angle 1.04707 / 0.49 (16047) SS BOND : bond 0.00167 / 0.08 ( 2) SS BOND : angle 0.52934 / 0.28 ( 4) hydrogen bonds : bond 0.28998 / 18.97 ( 399) hydrogen bonds : angle 9.30366 / 6.33 ( 1149) Misc. bond : bond 0.42969 / 22.62 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: C 186 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.6775 (ttm-80) REVERT: C 276 MET cc_start: 0.7076 (mmp) cc_final: 0.6629 (tpt) REVERT: C 281 ASP cc_start: 0.8265 (m-30) cc_final: 0.7838 (m-30) REVERT: C 386 GLN cc_start: 0.8952 (mt0) cc_final: 0.8512 (tp40) REVERT: D 46 GLU cc_start: 0.7821 (pm20) cc_final: 0.6782 (mm-30) REVERT: D 166 MET cc_start: 0.8189 (mmt) cc_final: 0.7814 (mmm) REVERT: B 418 LEU cc_start: 0.6701 (pt) cc_final: 0.6186 (tp) REVERT: B 529 MET cc_start: 0.8152 (mtp) cc_final: 0.7946 (mtt) REVERT: B 620 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6471 (tm-30) REVERT: A 445 LYS cc_start: 0.8613 (mtpt) cc_final: 0.7816 (mmpt) REVERT: A 716 ASP cc_start: 0.7675 (t0) cc_final: 0.7024 (m-30) outliers start: 8 outliers final: 3 residues processed: 175 average time/residue: 0.0996 time to fit residues: 24.9768 Evaluate side-chains 138 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 375 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 HIS ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.161023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122470 restraints weight = 35406.931| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 6.22 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11770 Z= 0.147 Angle : 0.682 8.935 16051 Z= 0.332 Chirality : 0.044 0.346 1847 Planarity : 0.005 0.077 1862 Dihedral : 13.221 117.061 1760 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.55 % Favored : 92.99 % Rotamer: Outliers : 0.94 % Allowed : 6.66 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.22), residues: 1315 helix: -1.87 (0.19), residues: 680 sheet: -0.45 (0.43), residues: 139 loop : -1.38 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 109 TYR 0.023 0.002 TYR A 496 PHE 0.015 0.002 PHE C 49 TRP 0.029 0.001 TRP C 65 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11767) covalent geometry : angle 0.68175 / 0.33 (16047) SS BOND : bond 0.00150 / 0.07 ( 2) SS BOND : angle 0.25047 / 0.12 ( 4) hydrogen bonds : bond 0.05555 / 3.57 ( 399) hydrogen bonds : angle 5.68039 / 3.87 ( 1149) Misc. bond : bond 0.00248 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.312 Fit side-chains REVERT: C 186 ARG cc_start: 0.7710 (ttm-80) cc_final: 0.7409 (ttm-80) REVERT: C 190 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7358 (m-30) REVERT: C 276 MET cc_start: 0.6810 (mmp) cc_final: 0.6415 (tpt) REVERT: C 334 MET cc_start: 0.8786 (ttm) cc_final: 0.8438 (ttp) REVERT: D 46 GLU cc_start: 0.8054 (pm20) cc_final: 0.7172 (mm-30) REVERT: D 166 MET cc_start: 0.8193 (mmt) cc_final: 0.7949 (mmm) REVERT: B 428 MET cc_start: 0.8351 (mtm) cc_final: 0.7964 (mtm) REVERT: B 620 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6409 (tm-30) REVERT: A 445 LYS cc_start: 0.8796 (mtpt) cc_final: 0.7986 (mmpt) REVERT: A 716 ASP cc_start: 0.7717 (t0) cc_final: 0.7204 (m-30) outliers start: 11 outliers final: 7 residues processed: 152 average time/residue: 0.0879 time to fit residues: 19.5744 Evaluate side-chains 138 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain A residue 605 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 0.0060 chunk 106 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 25 optimal weight: 0.0060 chunk 97 optimal weight: 0.4980 overall best weight: 0.5012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 386 GLN D 163 ASN A 504 HIS ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.162386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123494 restraints weight = 35238.685| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 6.16 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11770 Z= 0.113 Angle : 0.605 10.098 16051 Z= 0.295 Chirality : 0.041 0.331 1847 Planarity : 0.004 0.064 1862 Dihedral : 12.235 117.470 1756 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.10 % Favored : 93.45 % Rotamer: Outliers : 1.20 % Allowed : 9.74 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.22), residues: 1315 helix: -1.50 (0.19), residues: 681 sheet: -0.42 (0.42), residues: 142 loop : -1.21 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.020 0.001 TYR A 598 PHE 0.014 0.001 PHE C 350 TRP 0.022 0.001 TRP C 65 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (11767) covalent geometry : angle 0.60534 / 0.30 (16047) SS BOND : bond 0.00047 / 0.02 ( 2) SS BOND : angle 0.13496 / 0.07 ( 4) hydrogen bonds : bond 0.04052 / 2.61 ( 399) hydrogen bonds : angle 4.92181 / 3.35 ( 1149) Misc. bond : bond 0.00072 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.412 Fit side-chains REVERT: C 186 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7141 (ttm-80) REVERT: C 190 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: C 276 MET cc_start: 0.6616 (mmp) cc_final: 0.6342 (tpt) REVERT: C 334 MET cc_start: 0.8784 (ttm) cc_final: 0.8446 (ttp) REVERT: C 363 TRP cc_start: 0.8163 (t60) cc_final: 0.7905 (t60) REVERT: D 46 GLU cc_start: 0.8111 (pm20) cc_final: 0.7248 (mm-30) REVERT: D 166 MET cc_start: 0.8114 (mmt) cc_final: 0.7859 (mmm) REVERT: B 428 MET cc_start: 0.8287 (mtm) cc_final: 0.8073 (mtm) REVERT: B 445 LYS cc_start: 0.8223 (tppt) cc_final: 0.7721 (mmmt) REVERT: B 620 GLU cc_start: 0.6727 (tm-30) cc_final: 0.6392 (tm-30) REVERT: A 716 ASP cc_start: 0.7734 (t0) cc_final: 0.7304 (m-30) outliers start: 14 outliers final: 11 residues processed: 151 average time/residue: 0.0949 time to fit residues: 21.0175 Evaluate side-chains 138 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 720 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 163 ASN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.181438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.142339 restraints weight = 25646.400| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 4.38 r_work: 0.3408 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11770 Z= 0.150 Angle : 0.625 11.950 16051 Z= 0.306 Chirality : 0.042 0.265 1847 Planarity : 0.004 0.064 1862 Dihedral : 12.003 117.933 1756 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.78 % Favored : 92.76 % Rotamer: Outliers : 1.54 % Allowed : 10.93 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.23), residues: 1315 helix: -1.38 (0.19), residues: 688 sheet: -0.48 (0.42), residues: 143 loop : -1.25 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 109 TYR 0.025 0.002 TYR A 598 PHE 0.018 0.001 PHE C 91 TRP 0.018 0.002 TRP C 65 HIS 0.006 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (11767) covalent geometry : angle 0.62524 / 0.31 (16047) SS BOND : bond 0.00097 / 0.05 ( 2) SS BOND : angle 0.20851 / 0.10 ( 4) hydrogen bonds : bond 0.03941 / 2.56 ( 399) hydrogen bonds : angle 4.73690 / 3.20 ( 1149) Misc. bond : bond 0.00092 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.403 Fit side-chains REVERT: C 186 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7461 (ttm-80) REVERT: C 190 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8035 (m-30) REVERT: C 276 MET cc_start: 0.6712 (mmp) cc_final: 0.6410 (tpt) REVERT: C 334 MET cc_start: 0.8764 (ttm) cc_final: 0.8402 (ttp) REVERT: C 386 GLN cc_start: 0.8857 (mm110) cc_final: 0.8516 (tp40) REVERT: D 46 GLU cc_start: 0.7904 (pm20) cc_final: 0.6889 (mm-30) REVERT: D 166 MET cc_start: 0.8409 (mmt) cc_final: 0.8121 (mmm) REVERT: B 428 MET cc_start: 0.8376 (mtm) cc_final: 0.8166 (mtm) REVERT: B 445 LYS cc_start: 0.8239 (tppt) cc_final: 0.7770 (mmmt) REVERT: B 620 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7155 (tm-30) REVERT: A 642 TRP cc_start: 0.7470 (m-10) cc_final: 0.7199 (m-90) REVERT: A 716 ASP cc_start: 0.7877 (t0) cc_final: 0.7318 (m-30) outliers start: 18 outliers final: 14 residues processed: 145 average time/residue: 0.0833 time to fit residues: 17.9845 Evaluate side-chains 144 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 720 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 89 optimal weight: 5.9990 chunk 25 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 40 GLN D 99 HIS D 163 ASN B 652 HIS ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.173158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136895 restraints weight = 26886.607| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 4.67 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11770 Z= 0.178 Angle : 0.642 11.236 16051 Z= 0.315 Chirality : 0.043 0.159 1847 Planarity : 0.005 0.070 1862 Dihedral : 12.132 117.523 1756 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.55 % Favored : 92.99 % Rotamer: Outliers : 2.13 % Allowed : 12.04 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.23), residues: 1315 helix: -1.26 (0.20), residues: 690 sheet: -0.51 (0.42), residues: 144 loop : -1.36 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 109 TYR 0.020 0.002 TYR A 496 PHE 0.018 0.002 PHE C 91 TRP 0.017 0.002 TRP C 65 HIS 0.006 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (11767) covalent geometry : angle 0.64252 / 0.31 (16047) SS BOND : bond 0.00166 / 0.09 ( 2) SS BOND : angle 0.28191 / 0.13 ( 4) hydrogen bonds : bond 0.03915 / 2.54 ( 399) hydrogen bonds : angle 4.71758 / 3.18 ( 1149) Misc. bond : bond 0.00107 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.286 Fit side-chains REVERT: C 169 MET cc_start: 0.7440 (mtp) cc_final: 0.7208 (mtm) REVERT: C 186 ARG cc_start: 0.7565 (ttm-80) cc_final: 0.7125 (ttm-80) REVERT: C 190 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: D 46 GLU cc_start: 0.8037 (pm20) cc_final: 0.7216 (mm-30) REVERT: D 52 VAL cc_start: 0.8721 (m) cc_final: 0.8484 (t) REVERT: D 166 MET cc_start: 0.8344 (mmt) cc_final: 0.8119 (mmm) REVERT: D 226 MET cc_start: 0.8777 (mtp) cc_final: 0.8399 (mmm) REVERT: B 414 LYS cc_start: 0.6032 (tppt) cc_final: 0.4977 (tmtt) REVERT: B 620 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6636 (tm-30) REVERT: B 639 GLN cc_start: 0.7685 (mt0) cc_final: 0.7010 (mt0) REVERT: A 538 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7248 (t80) REVERT: A 716 ASP cc_start: 0.7838 (t0) cc_final: 0.7487 (m-30) outliers start: 25 outliers final: 16 residues processed: 148 average time/residue: 0.0897 time to fit residues: 19.2953 Evaluate side-chains 142 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 68 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 90 optimal weight: 0.0870 chunk 123 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 66 optimal weight: 0.0980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.175874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.138404 restraints weight = 21543.490| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 3.18 r_work: 0.3428 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11770 Z= 0.113 Angle : 0.592 12.305 16051 Z= 0.289 Chirality : 0.040 0.176 1847 Planarity : 0.004 0.072 1862 Dihedral : 11.553 117.167 1756 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.87 % Favored : 93.75 % Rotamer: Outliers : 1.88 % Allowed : 13.24 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.23), residues: 1315 helix: -1.08 (0.20), residues: 687 sheet: -0.57 (0.41), residues: 152 loop : -1.24 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 272 TYR 0.016 0.001 TYR A 598 PHE 0.017 0.001 PHE C 350 TRP 0.017 0.001 TRP C 385 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (11767) covalent geometry : angle 0.59166 / 0.29 (16047) SS BOND : bond 0.00026 / 0.01 ( 2) SS BOND : angle 0.08689 / 0.04 ( 4) hydrogen bonds : bond 0.03350 / 2.16 ( 399) hydrogen bonds : angle 4.45694 / 3.01 ( 1149) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.294 Fit side-chains REVERT: C 186 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7257 (ttm-80) REVERT: C 190 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: C 315 GLU cc_start: 0.7561 (mp0) cc_final: 0.7360 (mp0) REVERT: D 166 MET cc_start: 0.8456 (mmt) cc_final: 0.8183 (mmm) REVERT: B 414 LYS cc_start: 0.5984 (tppt) cc_final: 0.4888 (tmtt) REVERT: B 620 GLU cc_start: 0.7559 (tm-30) cc_final: 0.6855 (tm-30) REVERT: A 412 GLU cc_start: 0.7408 (pm20) cc_final: 0.7196 (pm20) REVERT: A 538 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7826 (t80) REVERT: A 715 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.6880 (mtp85) REVERT: A 716 ASP cc_start: 0.7870 (t0) cc_final: 0.7391 (m-30) outliers start: 22 outliers final: 16 residues processed: 149 average time/residue: 0.0855 time to fit residues: 19.0014 Evaluate side-chains 148 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 735 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 112 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 123 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 266 GLN ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.181593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.141442 restraints weight = 27357.762| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 4.49 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11770 Z= 0.132 Angle : 0.601 11.814 16051 Z= 0.294 Chirality : 0.041 0.175 1847 Planarity : 0.004 0.076 1862 Dihedral : 11.263 117.764 1756 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.25 % Favored : 93.37 % Rotamer: Outliers : 1.79 % Allowed : 13.92 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.23), residues: 1315 helix: -0.93 (0.20), residues: 681 sheet: -0.54 (0.41), residues: 153 loop : -1.23 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 109 TYR 0.017 0.001 TYR C 427 PHE 0.018 0.001 PHE C 350 TRP 0.017 0.001 TRP C 385 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (11767) covalent geometry : angle 0.60099 / 0.29 (16047) SS BOND : bond 0.00086 / 0.05 ( 2) SS BOND : angle 0.14701 / 0.06 ( 4) hydrogen bonds : bond 0.03405 / 2.21 ( 399) hydrogen bonds : angle 4.43607 / 2.99 ( 1149) Misc. bond : bond 0.00073 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.418 Fit side-chains REVERT: C 186 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.6898 (ttm-80) REVERT: C 190 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: C 386 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8157 (tp40) REVERT: D 166 MET cc_start: 0.8375 (mmt) cc_final: 0.8029 (mmm) REVERT: B 414 LYS cc_start: 0.5847 (tppt) cc_final: 0.4785 (tmtt) REVERT: B 620 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6642 (tm-30) REVERT: A 412 GLU cc_start: 0.7243 (pm20) cc_final: 0.6978 (pm20) REVERT: A 538 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7354 (t80) REVERT: A 716 ASP cc_start: 0.7881 (t0) cc_final: 0.7488 (m-30) outliers start: 21 outliers final: 16 residues processed: 145 average time/residue: 0.0885 time to fit residues: 19.2125 Evaluate side-chains 146 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 735 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.174786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137653 restraints weight = 28271.693| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 4.91 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11770 Z= 0.139 Angle : 0.615 12.447 16051 Z= 0.297 Chirality : 0.041 0.167 1847 Planarity : 0.004 0.082 1862 Dihedral : 10.994 117.599 1754 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.10 % Favored : 93.52 % Rotamer: Outliers : 1.88 % Allowed : 14.09 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.23), residues: 1315 helix: -0.83 (0.20), residues: 680 sheet: -0.62 (0.41), residues: 155 loop : -1.23 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 109 TYR 0.016 0.001 TYR A 496 PHE 0.016 0.001 PHE C 350 TRP 0.027 0.001 TRP C 385 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (11767) covalent geometry : angle 0.61541 / 0.30 (16047) SS BOND : bond 0.00096 / 0.05 ( 2) SS BOND : angle 0.17056 / 0.06 ( 4) hydrogen bonds : bond 0.03412 / 2.22 ( 399) hydrogen bonds : angle 4.43470 / 3.00 ( 1149) Misc. bond : bond 0.00070 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.441 Fit side-chains REVERT: C 186 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7011 (ttm-80) REVERT: C 190 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: D 166 MET cc_start: 0.8373 (mmt) cc_final: 0.8067 (mmm) REVERT: B 414 LYS cc_start: 0.6059 (tppt) cc_final: 0.5023 (tmtt) REVERT: B 620 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6612 (tm-30) REVERT: A 412 GLU cc_start: 0.7364 (pm20) cc_final: 0.7108 (pm20) REVERT: A 538 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7264 (t80) outliers start: 22 outliers final: 16 residues processed: 150 average time/residue: 0.0942 time to fit residues: 20.6660 Evaluate side-chains 153 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.175877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138574 restraints weight = 32327.332| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 5.64 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3807 r_free = 0.3807 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3807 r_free = 0.3807 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11770 Z= 0.126 Angle : 0.614 12.977 16051 Z= 0.298 Chirality : 0.041 0.168 1847 Planarity : 0.004 0.083 1862 Dihedral : 10.697 117.603 1752 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.02 % Favored : 93.60 % Rotamer: Outliers : 1.71 % Allowed : 14.60 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.23), residues: 1315 helix: -0.74 (0.20), residues: 683 sheet: -0.61 (0.41), residues: 155 loop : -1.22 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 611 TYR 0.019 0.001 TYR C 427 PHE 0.016 0.001 PHE C 350 TRP 0.026 0.001 TRP C 385 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (11767) covalent geometry : angle 0.61423 / 0.30 (16047) SS BOND : bond 0.00058 / 0.03 ( 2) SS BOND : angle 0.12487 / 0.06 ( 4) hydrogen bonds : bond 0.03292 / 2.14 ( 399) hydrogen bonds : angle 4.38197 / 2.97 ( 1149) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.411 Fit side-chains REVERT: C 186 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.6997 (ttm-80) REVERT: C 190 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: D 166 MET cc_start: 0.8387 (mmt) cc_final: 0.8073 (mmm) REVERT: D 226 MET cc_start: 0.8795 (mtp) cc_final: 0.8443 (mmm) REVERT: B 414 LYS cc_start: 0.6000 (tppt) cc_final: 0.4914 (tmtt) REVERT: B 620 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6520 (tm-30) REVERT: A 412 GLU cc_start: 0.7280 (pm20) cc_final: 0.7008 (pm20) REVERT: A 721 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7806 (tt) outliers start: 20 outliers final: 15 residues processed: 145 average time/residue: 0.0854 time to fit residues: 18.6100 Evaluate side-chains 144 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 44 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.174853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137270 restraints weight = 18124.785| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.77 r_work: 0.3448 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11770 Z= 0.144 Angle : 0.625 12.349 16051 Z= 0.302 Chirality : 0.041 0.166 1847 Planarity : 0.004 0.086 1862 Dihedral : 10.659 117.800 1752 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.33 % Favored : 93.29 % Rotamer: Outliers : 1.54 % Allowed : 14.94 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.23), residues: 1315 helix: -0.70 (0.20), residues: 686 sheet: -0.59 (0.41), residues: 153 loop : -1.28 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 109 TYR 0.015 0.001 TYR A 496 PHE 0.016 0.001 PHE C 91 TRP 0.031 0.001 TRP C 385 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (11767) covalent geometry : angle 0.62541 / 0.30 (16047) SS BOND : bond 0.00105 / 0.06 ( 2) SS BOND : angle 0.20958 / 0.08 ( 4) hydrogen bonds : bond 0.03402 / 2.22 ( 399) hydrogen bonds : angle 4.41103 / 2.98 ( 1149) Misc. bond : bond 0.00068 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.447 Fit side-chains REVERT: C 190 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7816 (m-30) REVERT: C 334 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8408 (mtm) REVERT: D 166 MET cc_start: 0.8438 (mmt) cc_final: 0.8182 (mmm) REVERT: B 414 LYS cc_start: 0.6093 (tppt) cc_final: 0.4998 (tmtt) REVERT: B 620 GLU cc_start: 0.7587 (tm-30) cc_final: 0.6918 (tm-30) REVERT: A 412 GLU cc_start: 0.7415 (pm20) cc_final: 0.7150 (pm20) REVERT: A 721 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7663 (tt) outliers start: 18 outliers final: 15 residues processed: 140 average time/residue: 0.0775 time to fit residues: 16.2918 Evaluate side-chains 145 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 17 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 102 optimal weight: 0.0470 chunk 66 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127444 restraints weight = 30156.313| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 5.59 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11770 Z= 0.106 Angle : 0.594 12.308 16051 Z= 0.287 Chirality : 0.040 0.166 1847 Planarity : 0.004 0.086 1862 Dihedral : 10.237 117.197 1752 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.34 % Favored : 94.28 % Rotamer: Outliers : 1.54 % Allowed : 14.94 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.23), residues: 1315 helix: -0.50 (0.21), residues: 675 sheet: -0.44 (0.41), residues: 153 loop : -1.17 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 528 TYR 0.015 0.001 TYR C 427 PHE 0.016 0.001 PHE C 350 TRP 0.032 0.001 TRP C 385 HIS 0.004 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (11767) covalent geometry : angle 0.59453 / 0.29 (16047) SS BOND : bond 0.00015 / 0.01 ( 2) SS BOND : angle 0.17789 / 0.09 ( 4) hydrogen bonds : bond 0.02971 / 1.92 ( 399) hydrogen bonds : angle 4.25765 / 2.89 ( 1149) Misc. bond : bond 0.00053 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2228.62 seconds wall clock time: 38 minutes 58.02 seconds (2338.02 seconds total)