Starting phenix.real_space_refine on Sat Jul 4 10:52:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t1d_40960/07_2026/8t1d_40960.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1d_40960/07_2026/8t1d_40960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t1d_40960/07_2026/8t1d_40960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1d_40960/07_2026/8t1d_40960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t1d_40960/07_2026/8t1d_40960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1d_40960/07_2026/8t1d_40960.map" } resolution = 3.35 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 13268 2.51 5 N 3344 2.21 5 O 3622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s 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: 20338 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 5086 Classifications: {'peptide': 632} Link IDs: {'PTRANS': 25, 'TRANS': 606} Chain breaks: 1 Chain: "B" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4987 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 24, 'TRANS': 594} Chain breaks: 2 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'XS9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'XS9': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D Time building chain proxies: 7.27, per 1000 atoms: 0.36 Number of scatterers: 20338 At special positions: 0 Unit cell: (145.928, 153.816, 124.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 3622 8.00 N 3344 7.00 C 13268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 639 " - pdb=" SG CYS A 660 " distance=2.03 Simple disulfide: pdb=" SG CYS B 639 " - pdb=" SG CYS B 660 " distance=2.03 Simple disulfide: pdb=" SG CYS C 639 " - pdb=" SG CYS C 660 " distance=2.03 Simple disulfide: pdb=" SG CYS D 639 " - pdb=" SG CYS D 660 " 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=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 787.0 milliseconds 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 4 sheets defined 62.2% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.700A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 removed outlier: 3.806A pdb=" N LEU A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 removed outlier: 3.564A pdb=" N PHE A 185 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 186 " --> pdb=" O GLU A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 186' Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.866A pdb=" N LYS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 4.420A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.910A pdb=" N ILE A 227 " --> pdb=" O MET A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.654A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.614A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.566A pdb=" N THR A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 337 through 356 removed outlier: 4.329A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.593A pdb=" N ALA A 364 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.754A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 removed outlier: 3.593A pdb=" N VAL A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 451 removed outlier: 4.223A pdb=" N ALA A 451 " --> pdb=" O HIS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 removed outlier: 3.665A pdb=" N LEU A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 491 removed outlier: 3.542A pdb=" N VAL A 476 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 524 removed outlier: 3.993A pdb=" N VAL A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.889A pdb=" N ASN A 528 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 529 " --> pdb=" O PHE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 569 removed outlier: 3.924A pdb=" N ILE A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 removed outlier: 4.017A pdb=" N VAL A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 removed outlier: 3.711A pdb=" N THR A 593 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 594 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 613 removed outlier: 3.549A pdb=" N SER A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 632 removed outlier: 3.685A pdb=" N PHE A 617 " --> pdb=" O ASP A 613 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 628 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 removed outlier: 4.230A pdb=" N SER A 659 " --> pdb=" O THR A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 675 removed outlier: 3.670A pdb=" N LEU A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 706 removed outlier: 4.433A pdb=" N ILE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 722 removed outlier: 3.734A pdb=" N GLU A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 722 " --> pdb=" O MET A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 748 removed outlier: 3.534A pdb=" N HIS A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 741 " --> pdb=" O TRP A 737 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 757 removed outlier: 3.578A pdb=" N ARG A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.795A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 176 removed outlier: 3.647A pdb=" N HIS B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.523A pdb=" N LYS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.888A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.694A pdb=" N ASN B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.910A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 260 removed outlier: 3.775A pdb=" N VAL B 254 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.801A pdb=" N GLY B 279 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.559A pdb=" N ALA B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 323 through 331 removed outlier: 3.679A pdb=" N VAL B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 356 removed outlier: 4.320A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 380 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.855A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.550A pdb=" N ILE B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 453 through 464 removed outlier: 4.065A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 491 removed outlier: 3.609A pdb=" N ILE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR B 478 " --> pdb=" O ASN B 474 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 530 removed outlier: 3.560A pdb=" N GLU B 514 " --> pdb=" O ARG B 510 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 569 removed outlier: 3.918A pdb=" N LEU B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 560 " --> pdb=" O TYR B 556 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 568 " --> pdb=" O ALA B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 590 removed outlier: 3.718A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 602 Processing helix chain 'B' and resid 604 through 633 removed outlier: 4.564A pdb=" N LYS B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 611 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 612 " --> pdb=" O LYS B 608 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 613 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 630 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 4.480A pdb=" N LEU B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 705 removed outlier: 4.040A pdb=" N ILE B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 721 Processing helix chain 'B' and resid 721 through 728 removed outlier: 3.788A pdb=" N VAL B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 746 removed outlier: 3.802A pdb=" N TRP B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU B 735 " --> pdb=" O HIS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 756 Processing helix chain 'B' and resid 785 through 791 removed outlier: 4.089A pdb=" N GLN B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN B 791 " --> pdb=" O HIS B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.700A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP C 156 " --> pdb=" O PRO C 152 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 176 removed outlier: 3.805A pdb=" N LEU C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 removed outlier: 3.564A pdb=" N PHE C 185 " --> pdb=" O ASP C 182 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 186 " --> pdb=" O GLU C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 182 through 186' Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.866A pdb=" N LYS C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 removed outlier: 4.421A pdb=" N VAL C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 3.910A pdb=" N ILE C 227 " --> pdb=" O MET C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.654A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 260 removed outlier: 3.614A pdb=" N VAL C 254 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.566A pdb=" N THR C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 330 Processing helix chain 'C' and resid 337 through 356 removed outlier: 4.329A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 removed outlier: 3.593A pdb=" N ALA C 364 " --> pdb=" O ASN C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.754A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 439 removed outlier: 3.594A pdb=" N VAL C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 451 removed outlier: 4.222A pdb=" N ALA C 451 " --> pdb=" O HIS C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 466 removed outlier: 3.665A pdb=" N LEU C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 460 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 491 removed outlier: 3.541A pdb=" N VAL C 476 " --> pdb=" O TYR C 472 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE C 484 " --> pdb=" O CYS C 480 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 524 removed outlier: 3.993A pdb=" N VAL C 515 " --> pdb=" O LEU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.890A pdb=" N ASN C 528 " --> pdb=" O PHE C 524 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 529 " --> pdb=" O PHE C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 569 removed outlier: 3.924A pdb=" N ILE C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 588 removed outlier: 4.017A pdb=" N VAL C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.711A pdb=" N THR C 593 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 594 " --> pdb=" O TYR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 613 removed outlier: 3.548A pdb=" N SER C 603 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 606 " --> pdb=" O TYR C 602 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 607 " --> pdb=" O SER C 603 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 632 removed outlier: 3.685A pdb=" N PHE C 617 " --> pdb=" O ASP C 613 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 620 " --> pdb=" O ARG C 616 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 628 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 630 " --> pdb=" O ILE C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 removed outlier: 4.231A pdb=" N SER C 659 " --> pdb=" O THR C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 675 removed outlier: 3.670A pdb=" N LEU C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 706 removed outlier: 4.433A pdb=" N ILE C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 722 removed outlier: 3.734A pdb=" N GLU C 720 " --> pdb=" O ALA C 716 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 722 " --> pdb=" O MET C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 748 removed outlier: 3.534A pdb=" N HIS C 731 " --> pdb=" O LYS C 727 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 741 " --> pdb=" O TRP C 737 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 742 " --> pdb=" O ALA C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 757 removed outlier: 3.578A pdb=" N ARG C 757 " --> pdb=" O ARG C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 791 Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.796A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 161 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 176 removed outlier: 3.646A pdb=" N HIS D 176 " --> pdb=" O PHE D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.522A pdb=" N LYS D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.888A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 removed outlier: 3.694A pdb=" N ASN D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.910A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 260 removed outlier: 3.774A pdb=" N VAL D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.801A pdb=" N GLY D 279 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 removed outlier: 3.560A pdb=" N ALA D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 304 Processing helix chain 'D' and resid 323 through 331 removed outlier: 3.680A pdb=" N VAL D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 356 removed outlier: 4.320A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 380 Processing helix chain 'D' and resid 383 through 391 removed outlier: 3.855A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 389 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 437 removed outlier: 3.549A pdb=" N ILE D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 450 Processing helix chain 'D' and resid 453 through 464 removed outlier: 4.065A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 491 removed outlier: 3.610A pdb=" N ILE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR D 478 " --> pdb=" O ASN D 474 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 481 " --> pdb=" O SER D 477 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 530 removed outlier: 3.561A pdb=" N GLU D 514 " --> pdb=" O ARG D 510 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL D 515 " --> pdb=" O LEU D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 569 removed outlier: 3.917A pdb=" N LEU D 552 " --> pdb=" O SER D 548 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR D 553 " --> pdb=" O PHE D 549 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 560 " --> pdb=" O TYR D 556 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 568 " --> pdb=" O ALA D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 590 removed outlier: 3.717A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 584 " --> pdb=" O PHE D 580 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 586 " --> pdb=" O LEU D 582 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 602 Processing helix chain 'D' and resid 604 through 633 removed outlier: 4.564A pdb=" N LYS D 608 " --> pdb=" O ILE D 604 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE D 611 " --> pdb=" O GLN D 607 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP D 613 " --> pdb=" O ILE D 609 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE D 615 " --> pdb=" O PHE D 611 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL D 620 " --> pdb=" O ARG D 616 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 626 " --> pdb=" O LEU D 622 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 627 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 630 " --> pdb=" O ILE D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 679 removed outlier: 4.479A pdb=" N LEU D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 705 removed outlier: 4.040A pdb=" N ILE D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 721 Processing helix chain 'D' and resid 721 through 728 removed outlier: 3.787A pdb=" N VAL D 725 " --> pdb=" O THR D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 746 removed outlier: 3.801A pdb=" N TRP D 733 " --> pdb=" O SER D 729 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU D 735 " --> pdb=" O HIS D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 Processing helix chain 'D' and resid 785 through 791 removed outlier: 4.088A pdb=" N GLN D 790 " --> pdb=" O SER D 786 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN D 791 " --> pdb=" O HIS D 787 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 409 removed outlier: 7.129A pdb=" N SER A 416 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 775 " --> pdb=" O VAL A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 406 through 407 Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 409 removed outlier: 7.129A pdb=" N SER C 416 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG C 775 " --> pdb=" O VAL C 762 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 406 through 407 846 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3328 1.32 - 1.44: 5606 1.44 - 1.57: 11719 1.57 - 1.69: 1 1.69 - 1.81: 170 Bond restraints: 20824 Sorted by residual: bond pdb=" C TYR C 657 " pdb=" N PRO C 658 " ideal model delta sigma weight residual 1.337 1.399 -0.063 9.80e-03 1.04e+04 4.08e+01 bond pdb=" C TYR A 657 " pdb=" N PRO A 658 " ideal model delta sigma weight residual 1.337 1.399 -0.062 9.80e-03 1.04e+04 4.06e+01 bond pdb=" C TYR B 657 " pdb=" N PRO B 658 " ideal model delta sigma weight residual 1.337 1.385 -0.048 9.80e-03 1.04e+04 2.41e+01 bond pdb=" C TYR D 657 " pdb=" N PRO D 658 " ideal model delta sigma weight residual 1.337 1.385 -0.048 9.80e-03 1.04e+04 2.41e+01 bond pdb=" C LEU C 170 " pdb=" N PRO C 171 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.36e-02 5.41e+03 2.06e+01 ... (remaining 20819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 27859 4.41 - 8.82: 369 8.82 - 13.23: 34 13.23 - 17.64: 6 17.64 - 22.05: 4 Bond angle restraints: 28272 Sorted by residual: angle pdb=" C SER A 663 " pdb=" N GLU A 664 " pdb=" CA GLU A 664 " ideal model delta sigma weight residual 121.54 136.57 -15.03 1.91e+00 2.74e-01 6.19e+01 angle pdb=" C SER C 663 " pdb=" N GLU C 664 " pdb=" CA GLU C 664 " ideal model delta sigma weight residual 121.54 136.55 -15.01 1.91e+00 2.74e-01 6.17e+01 angle pdb=" C ASP C 662 " pdb=" N SER C 663 " pdb=" CA SER C 663 " ideal model delta sigma weight residual 121.54 133.93 -12.39 1.91e+00 2.74e-01 4.21e+01 angle pdb=" C ASP A 662 " pdb=" N SER A 663 " pdb=" CA SER A 663 " ideal model delta sigma weight residual 121.54 133.91 -12.37 1.91e+00 2.74e-01 4.20e+01 angle pdb=" CA LEU B 494 " pdb=" CB LEU B 494 " pdb=" CG LEU B 494 " ideal model delta sigma weight residual 116.30 138.35 -22.05 3.50e+00 8.16e-02 3.97e+01 ... (remaining 28267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.04: 12236 29.04 - 58.08: 390 58.08 - 87.12: 28 87.12 - 116.15: 6 116.15 - 145.19: 6 Dihedral angle restraints: 12666 sinusoidal: 5330 harmonic: 7336 Sorted by residual: dihedral pdb=" CA GLU C 453 " pdb=" C GLU C 453 " pdb=" N PRO C 454 " pdb=" CA PRO C 454 " ideal model delta harmonic sigma weight residual 180.00 -127.45 -52.55 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA GLU A 453 " pdb=" C GLU A 453 " pdb=" N PRO A 454 " pdb=" CA PRO A 454 " ideal model delta harmonic sigma weight residual -180.00 -127.45 -52.55 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA GLU C 664 " pdb=" C GLU C 664 " pdb=" N THR C 665 " pdb=" CA THR C 665 " ideal model delta harmonic sigma weight residual 180.00 127.88 52.12 0 5.00e+00 4.00e-02 1.09e+02 ... (remaining 12663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2800 0.080 - 0.159: 349 0.159 - 0.239: 51 0.239 - 0.319: 19 0.319 - 0.398: 7 Chirality restraints: 3226 Sorted by residual: chirality pdb=" C15 XS9 A1201 " pdb=" C14 XS9 A1201 " pdb=" C16 XS9 A1201 " pdb=" C21 XS9 A1201 " both_signs ideal model delta sigma weight residual False -2.86 -2.46 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C15 XS9 C1201 " pdb=" C14 XS9 C1201 " pdb=" C16 XS9 C1201 " pdb=" C21 XS9 C1201 " both_signs ideal model delta sigma weight residual False -2.86 -2.46 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CG LEU A 614 " pdb=" CB LEU A 614 " pdb=" CD1 LEU A 614 " pdb=" CD2 LEU A 614 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 3223 not shown) Planarity restraints: 3512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 453 " -0.064 5.00e-02 4.00e+02 9.70e-02 1.50e+01 pdb=" N PRO C 454 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 454 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 454 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 453 " 0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A 454 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 665 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C THR A 665 " -0.055 2.00e-02 2.50e+03 pdb=" O THR A 665 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE A 666 " 0.019 2.00e-02 2.50e+03 ... (remaining 3509 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1090 2.72 - 3.26: 20262 3.26 - 3.81: 32510 3.81 - 4.35: 40900 4.35 - 4.90: 66757 Nonbonded interactions: 161519 Sorted by model distance: nonbonded pdb=" O TYR D 702 " pdb=" OG1 THR D 706 " model vdw 2.170 3.040 nonbonded pdb=" O TYR B 702 " pdb=" OG1 THR B 706 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR D 220 " pdb=" OD1 ASN D 222 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR B 220 " pdb=" OD1 ASN B 222 " model vdw 2.276 3.040 nonbonded pdb=" O GLU D 225 " pdb=" OG SER D 229 " model vdw 2.283 3.040 ... (remaining 161514 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.710 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 : 0.006 0.102 20828 Z= 0.318 Angle : 1.368 22.051 28280 Z= 0.773 Chirality : 0.061 0.398 3226 Planarity : 0.008 0.097 3512 Dihedral : 13.832 145.192 7926 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.64 % Allowed : 12.21 % Favored : 87.15 % Rotamer: Outliers : 0.72 % Allowed : 7.97 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.75 % 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: -5.63 (0.12), residues: 2482 helix: -3.95 (0.08), residues: 1346 sheet: -3.21 (0.49), residues: 74 loop : -3.31 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 404 TYR 0.025 0.002 TYR A 236 PHE 0.033 0.003 PHE D 185 TRP 0.027 0.002 TRP C 733 HIS 0.005 0.001 HIS D 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.32 (20824) covalent geometry : angle 1.36748 / 0.77 (28272) SS BOND : bond 0.00264 / 0.13 ( 4) SS BOND : angle 3.00033 / 1.64 ( 8) hydrogen bonds : bond 0.30218 / 20.11 ( 846) hydrogen bonds : angle 9.83966 / 6.81 ( 2490) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 675 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ASP cc_start: 0.8216 (t70) cc_final: 0.8011 (t70) REVERT: A 621 TYR cc_start: 0.8300 (t80) cc_final: 0.8026 (t80) REVERT: A 734 LYS cc_start: 0.8652 (tppp) cc_final: 0.8236 (tppt) REVERT: B 182 ASP cc_start: 0.6851 (m-30) cc_final: 0.6615 (m-30) REVERT: B 260 GLN cc_start: 0.8827 (mp-120) cc_final: 0.8603 (mp10) REVERT: B 457 GLU cc_start: 0.7447 (mp0) cc_final: 0.7089 (mp0) REVERT: B 549 PHE cc_start: 0.7035 (m-80) cc_final: 0.6740 (m-80) REVERT: B 612 LYS cc_start: 0.8740 (ttpm) cc_final: 0.8333 (ttpt) REVERT: B 625 MET cc_start: 0.8271 (ttp) cc_final: 0.7812 (mtp) REVERT: B 713 MET cc_start: 0.8605 (mmm) cc_final: 0.8275 (mmm) REVERT: C 621 TYR cc_start: 0.8260 (t80) cc_final: 0.7892 (t80) REVERT: C 635 LEU cc_start: 0.8464 (mt) cc_final: 0.8225 (mp) REVERT: C 685 MET cc_start: 0.6971 (tpt) cc_final: 0.6659 (ppp) REVERT: C 705 LEU cc_start: 0.8993 (mp) cc_final: 0.8680 (mp) REVERT: C 734 LYS cc_start: 0.8690 (tppp) cc_final: 0.8127 (tppt) REVERT: D 182 ASP cc_start: 0.6807 (m-30) cc_final: 0.6606 (m-30) REVERT: D 278 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6986 (tm-30) REVERT: D 346 TYR cc_start: 0.8118 (t80) cc_final: 0.7604 (t80) REVERT: D 457 GLU cc_start: 0.7594 (mp0) cc_final: 0.6940 (mp0) REVERT: D 461 ASP cc_start: 0.8261 (t70) cc_final: 0.7906 (t70) REVERT: D 517 THR cc_start: 0.8979 (m) cc_final: 0.8664 (p) REVERT: D 625 MET cc_start: 0.7947 (ttp) cc_final: 0.7469 (mtm) REVERT: D 730 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8773 (mmmt) outliers start: 16 outliers final: 2 residues processed: 685 average time/residue: 0.1360 time to fit residues: 141.1929 Evaluate side-chains 436 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 434 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain D residue 421 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.3980 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 207 ASN A 228 ASN A 260 GLN A 274 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 474 ASN A 712 ASN B 204 ASN B 207 ASN B 260 GLN B 326 HIS B 361 ASN B 401 HIS B 456 ASN B 492 GLN B 550 GLN B 736 GLN C 228 ASN C 260 GLN C 274 GLN C 297 GLN C 456 ASN C 474 ASN C 712 ASN D 207 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN D 326 HIS D 361 ASN D 401 HIS D 456 ASN D 492 GLN D 550 GLN D 787 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.183368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.132509 restraints weight = 33081.894| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.33 r_work: 0.3495 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 20828 Z= 0.242 Angle : 0.902 14.315 28280 Z= 0.458 Chirality : 0.048 0.410 3226 Planarity : 0.006 0.080 3512 Dihedral : 11.177 82.622 3168 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.64 % Favored : 87.79 % Rotamer: Outliers : 4.17 % Allowed : 13.63 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.67 % 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: -3.74 (0.15), residues: 2482 helix: -2.03 (0.11), residues: 1424 sheet: -3.16 (0.50), residues: 74 loop : -2.99 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 757 TYR 0.031 0.002 TYR B 283 PHE 0.038 0.002 PHE B 284 TRP 0.025 0.002 TRP A 733 HIS 0.008 0.001 HIS D 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 (20824) covalent geometry : angle 0.90183 / 0.46 (28272) SS BOND : bond 0.00908 / 0.44 ( 4) SS BOND : angle 1.68587 / 0.99 ( 8) hydrogen bonds : bond 0.05105 / 3.41 ( 846) hydrogen bonds : angle 5.26505 / 3.67 ( 2490) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 462 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.8595 (t70) cc_final: 0.8131 (t70) REVERT: A 234 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7940 (mm) REVERT: A 271 ARG cc_start: 0.8131 (ttm110) cc_final: 0.7914 (mmm-85) REVERT: A 347 ASP cc_start: 0.8335 (m-30) cc_final: 0.8077 (m-30) REVERT: A 393 GLU cc_start: 0.8313 (pm20) cc_final: 0.8106 (pm20) REVERT: A 445 ASN cc_start: 0.7740 (m110) cc_final: 0.7518 (m-40) REVERT: A 456 ASN cc_start: 0.8777 (t0) cc_final: 0.8435 (t0) REVERT: A 461 ASP cc_start: 0.8601 (t70) cc_final: 0.8203 (t70) REVERT: A 534 MET cc_start: 0.6130 (tpp) cc_final: 0.5313 (mtt) REVERT: A 559 LEU cc_start: 0.7169 (mp) cc_final: 0.6920 (tt) REVERT: A 591 TYR cc_start: 0.8556 (t80) cc_final: 0.7943 (t80) REVERT: A 685 MET cc_start: 0.8103 (tpp) cc_final: 0.7367 (ptp) REVERT: A 711 LEU cc_start: 0.9486 (mm) cc_final: 0.9240 (mm) REVERT: A 713 MET cc_start: 0.8650 (mmm) cc_final: 0.8258 (mmt) REVERT: A 734 LYS cc_start: 0.8888 (tppp) cc_final: 0.8489 (tppt) REVERT: B 182 ASP cc_start: 0.6804 (m-30) cc_final: 0.6510 (m-30) REVERT: B 278 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7490 (tm-30) REVERT: B 345 MET cc_start: 0.8977 (mtt) cc_final: 0.8767 (mtp) REVERT: B 346 TYR cc_start: 0.8461 (t80) cc_final: 0.7901 (t80) REVERT: B 549 PHE cc_start: 0.6988 (m-80) cc_final: 0.6697 (m-80) REVERT: B 605 MET cc_start: 0.8366 (tmm) cc_final: 0.7864 (ppp) REVERT: B 606 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.7953 (pp) REVERT: B 621 TYR cc_start: 0.7198 (t80) cc_final: 0.6935 (t80) REVERT: B 685 MET cc_start: 0.4506 (ptt) cc_final: 0.4246 (ptm) REVERT: B 728 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8408 (mt-10) REVERT: C 234 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7421 (mm) REVERT: C 347 ASP cc_start: 0.8320 (m-30) cc_final: 0.8095 (m-30) REVERT: C 363 GLU cc_start: 0.7673 (tt0) cc_final: 0.7284 (tt0) REVERT: C 612 LYS cc_start: 0.7697 (mmtm) cc_final: 0.7395 (tttp) REVERT: C 685 MET cc_start: 0.7615 (tpt) cc_final: 0.7126 (ppp) REVERT: C 734 LYS cc_start: 0.8919 (tppp) cc_final: 0.8455 (tppt) REVERT: C 774 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.8022 (mmm-85) REVERT: D 182 ASP cc_start: 0.6758 (m-30) cc_final: 0.6411 (m-30) REVERT: D 200 LEU cc_start: 0.7344 (mp) cc_final: 0.7049 (mp) REVERT: D 222 ASN cc_start: 0.7683 (p0) cc_final: 0.7341 (p0) REVERT: D 278 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7200 (tm-30) REVERT: D 461 ASP cc_start: 0.8938 (t70) cc_final: 0.8498 (t70) REVERT: D 517 THR cc_start: 0.8953 (m) cc_final: 0.8663 (p) REVERT: D 551 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8291 (mm) REVERT: D 606 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7962 (pp) REVERT: D 625 MET cc_start: 0.8117 (ttp) cc_final: 0.7836 (mtp) REVERT: D 669 PHE cc_start: 0.8733 (t80) cc_final: 0.8459 (t80) REVERT: D 730 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8616 (mmmt) outliers start: 92 outliers final: 52 residues processed: 515 average time/residue: 0.1156 time to fit residues: 95.0781 Evaluate side-chains 462 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 405 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 704 ILE Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 768 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 219 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 113 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 246 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN B 204 ASN C 201 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN D 492 GLN D 791 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.187470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138705 restraints weight = 33247.418| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.30 r_work: 0.3559 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20828 Z= 0.147 Angle : 0.795 14.088 28280 Z= 0.397 Chirality : 0.043 0.209 3226 Planarity : 0.005 0.071 3512 Dihedral : 9.351 69.517 3164 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.00 % Favored : 88.48 % Rotamer: Outliers : 3.67 % Allowed : 17.26 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.58 % 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: -2.84 (0.16), residues: 2482 helix: -1.22 (0.12), residues: 1434 sheet: -2.79 (0.52), residues: 74 loop : -2.74 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 616 TYR 0.048 0.002 TYR A 657 PHE 0.029 0.002 PHE B 284 TRP 0.021 0.002 TRP A 733 HIS 0.007 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (20824) covalent geometry : angle 0.79452 / 0.40 (28272) SS BOND : bond 0.00087 / 0.04 ( 4) SS BOND : angle 1.33380 / 0.78 ( 8) hydrogen bonds : bond 0.04167 / 2.77 ( 846) hydrogen bonds : angle 4.78687 / 3.34 ( 2490) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 451 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7780 (mm) REVERT: A 347 ASP cc_start: 0.8074 (m-30) cc_final: 0.7768 (m-30) REVERT: A 393 GLU cc_start: 0.8216 (pm20) cc_final: 0.8008 (pm20) REVERT: A 456 ASN cc_start: 0.8712 (t0) cc_final: 0.8422 (t0) REVERT: A 461 ASP cc_start: 0.8512 (t70) cc_final: 0.8173 (t70) REVERT: A 480 CYS cc_start: 0.8709 (m) cc_final: 0.8177 (t) REVERT: A 685 MET cc_start: 0.8007 (tpp) cc_final: 0.7251 (ptp) REVERT: A 734 LYS cc_start: 0.8894 (tppp) cc_final: 0.8494 (tppt) REVERT: B 278 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7439 (tm-30) REVERT: B 346 TYR cc_start: 0.8424 (t80) cc_final: 0.7641 (t80) REVERT: B 612 LYS cc_start: 0.8761 (ttpm) cc_final: 0.8479 (ttpt) REVERT: B 621 TYR cc_start: 0.7174 (t80) cc_final: 0.6843 (t80) REVERT: B 685 MET cc_start: 0.4458 (ptt) cc_final: 0.4175 (ptm) REVERT: B 782 GLU cc_start: 0.8582 (tt0) cc_final: 0.8197 (pt0) REVERT: C 234 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7201 (mm) REVERT: C 347 ASP cc_start: 0.8222 (m-30) cc_final: 0.7978 (m-30) REVERT: C 363 GLU cc_start: 0.7443 (tt0) cc_final: 0.6801 (tp30) REVERT: C 612 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7397 (tttp) REVERT: C 685 MET cc_start: 0.7564 (tpt) cc_final: 0.7132 (ppp) REVERT: C 705 LEU cc_start: 0.9099 (mp) cc_final: 0.8873 (mp) REVERT: C 734 LYS cc_start: 0.8934 (tppp) cc_final: 0.8454 (tppt) REVERT: D 200 LEU cc_start: 0.7394 (mp) cc_final: 0.7053 (mp) REVERT: D 278 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7170 (tm-30) REVERT: D 346 TYR cc_start: 0.8428 (t80) cc_final: 0.8220 (t80) REVERT: D 387 GLN cc_start: 0.8614 (mt0) cc_final: 0.8401 (pt0) REVERT: D 461 ASP cc_start: 0.8994 (t70) cc_final: 0.8588 (t70) REVERT: D 517 THR cc_start: 0.8948 (m) cc_final: 0.8656 (p) REVERT: D 551 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8495 (mm) REVERT: D 625 MET cc_start: 0.8138 (ttp) cc_final: 0.7862 (mtp) REVERT: D 669 PHE cc_start: 0.8676 (t80) cc_final: 0.8366 (t80) REVERT: D 730 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8607 (mmmt) outliers start: 81 outliers final: 46 residues processed: 492 average time/residue: 0.1210 time to fit residues: 94.7092 Evaluate side-chains 445 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 396 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 768 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 66 optimal weight: 9.9990 chunk 209 optimal weight: 0.0170 chunk 222 optimal weight: 30.0000 chunk 177 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 239 optimal weight: 0.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN B 367 ASN C 207 ASN C 387 GLN D 201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.185795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136403 restraints weight = 33099.546| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.32 r_work: 0.3530 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20828 Z= 0.162 Angle : 0.782 12.208 28280 Z= 0.391 Chirality : 0.045 0.388 3226 Planarity : 0.005 0.065 3512 Dihedral : 8.541 61.925 3164 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.92 % Favored : 88.64 % Rotamer: Outliers : 4.39 % Allowed : 17.35 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.58 % 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: -2.31 (0.16), residues: 2482 helix: -0.69 (0.13), residues: 1408 sheet: -3.00 (0.48), residues: 92 loop : -2.60 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 774 TYR 0.030 0.002 TYR A 657 PHE 0.028 0.002 PHE D 284 TRP 0.014 0.001 TRP B 737 HIS 0.007 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (20824) covalent geometry : angle 0.78222 / 0.39 (28272) SS BOND : bond 0.00082 / 0.04 ( 4) SS BOND : angle 0.98859 / 0.57 ( 8) hydrogen bonds : bond 0.03678 / 2.44 ( 846) hydrogen bonds : angle 4.61143 / 3.20 ( 2490) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 421 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7871 (mm) REVERT: A 347 ASP cc_start: 0.8143 (m-30) cc_final: 0.7812 (m-30) REVERT: A 456 ASN cc_start: 0.8768 (t0) cc_final: 0.8520 (t0) REVERT: A 461 ASP cc_start: 0.8523 (t70) cc_final: 0.8159 (t70) REVERT: A 680 MET cc_start: 0.2283 (mtp) cc_final: 0.1306 (mmt) REVERT: A 711 LEU cc_start: 0.9418 (mm) cc_final: 0.9146 (mm) REVERT: A 734 LYS cc_start: 0.8929 (tppp) cc_final: 0.8525 (tptt) REVERT: B 182 ASP cc_start: 0.6795 (m-30) cc_final: 0.6458 (m-30) REVERT: B 278 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7425 (tm-30) REVERT: B 287 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8790 (mp) REVERT: B 601 THR cc_start: 0.8353 (m) cc_final: 0.8132 (m) REVERT: B 605 MET cc_start: 0.8059 (ppp) cc_final: 0.7543 (ppp) REVERT: B 612 LYS cc_start: 0.8742 (ttpm) cc_final: 0.8449 (ttpt) REVERT: B 685 MET cc_start: 0.4499 (ptt) cc_final: 0.4203 (ptm) REVERT: B 761 MET cc_start: 0.8584 (tpp) cc_final: 0.8357 (tpp) REVERT: B 782 GLU cc_start: 0.8610 (tt0) cc_final: 0.8255 (pt0) REVERT: C 234 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7242 (mm) REVERT: C 347 ASP cc_start: 0.8328 (m-30) cc_final: 0.8078 (m-30) REVERT: C 363 GLU cc_start: 0.7658 (tt0) cc_final: 0.6793 (tp30) REVERT: C 452 VAL cc_start: 0.6379 (OUTLIER) cc_final: 0.5324 (t) REVERT: C 612 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7391 (tttp) REVERT: C 616 ARG cc_start: 0.7562 (mtp180) cc_final: 0.7317 (tpt-90) REVERT: C 685 MET cc_start: 0.7624 (tpt) cc_final: 0.7179 (ppp) REVERT: C 705 LEU cc_start: 0.9116 (mp) cc_final: 0.8805 (mp) REVERT: C 734 LYS cc_start: 0.8952 (tppp) cc_final: 0.8537 (tppt) REVERT: D 200 LEU cc_start: 0.7415 (mp) cc_final: 0.7069 (mp) REVERT: D 278 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7224 (tm-30) REVERT: D 461 ASP cc_start: 0.8992 (t70) cc_final: 0.8593 (t70) REVERT: D 517 THR cc_start: 0.8978 (m) cc_final: 0.8672 (p) REVERT: D 551 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8487 (mm) REVERT: D 625 MET cc_start: 0.8169 (ttp) cc_final: 0.7787 (mtm) REVERT: D 669 PHE cc_start: 0.8683 (t80) cc_final: 0.8360 (t80) REVERT: D 730 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8578 (mmmt) outliers start: 97 outliers final: 70 residues processed: 471 average time/residue: 0.1162 time to fit residues: 87.5244 Evaluate side-chains 459 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 384 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 712 ASN Chi-restraints excluded: chain D residue 771 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 88 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 209 optimal weight: 0.0040 chunk 173 optimal weight: 30.0000 chunk 86 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN C 387 GLN C 528 ASN D 790 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.187688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138503 restraints weight = 33090.609| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.34 r_work: 0.3570 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20828 Z= 0.131 Angle : 0.749 12.648 28280 Z= 0.372 Chirality : 0.043 0.283 3226 Planarity : 0.005 0.053 3512 Dihedral : 8.012 58.707 3164 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.68 % Favored : 88.96 % Rotamer: Outliers : 4.21 % Allowed : 18.70 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.54 % 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: -1.89 (0.17), residues: 2482 helix: -0.34 (0.13), residues: 1420 sheet: -2.86 (0.50), residues: 92 loop : -2.44 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 269 TYR 0.032 0.001 TYR A 657 PHE 0.028 0.001 PHE D 284 TRP 0.015 0.001 TRP A 788 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (20824) covalent geometry : angle 0.74880 / 0.37 (28272) SS BOND : bond 0.00072 / 0.03 ( 4) SS BOND : angle 0.87939 / 0.50 ( 8) hydrogen bonds : bond 0.03355 / 2.24 ( 846) hydrogen bonds : angle 4.46576 / 3.10 ( 2490) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 434 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7237 (ttp-170) cc_final: 0.6937 (ttp-170) REVERT: A 228 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.6158 (p0) REVERT: A 234 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7787 (mm) REVERT: A 397 GLU cc_start: 0.8280 (pm20) cc_final: 0.7931 (tm-30) REVERT: A 685 MET cc_start: 0.8013 (tpp) cc_final: 0.7307 (ptp) REVERT: A 734 LYS cc_start: 0.8904 (tppp) cc_final: 0.8594 (tptt) REVERT: B 182 ASP cc_start: 0.6798 (m-30) cc_final: 0.6452 (m-30) REVERT: B 278 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 448 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7806 (mp0) REVERT: B 605 MET cc_start: 0.8137 (ppp) cc_final: 0.7548 (ppp) REVERT: B 612 LYS cc_start: 0.8725 (ttpm) cc_final: 0.8206 (pttt) REVERT: B 685 MET cc_start: 0.4373 (ptt) cc_final: 0.4089 (ptm) REVERT: B 713 MET cc_start: 0.8413 (mmm) cc_final: 0.8046 (tpt) REVERT: B 782 GLU cc_start: 0.8553 (tt0) cc_final: 0.8245 (pt0) REVERT: C 219 ARG cc_start: 0.8902 (mmp80) cc_final: 0.8699 (mmp80) REVERT: C 234 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7164 (mm) REVERT: C 347 ASP cc_start: 0.8323 (m-30) cc_final: 0.8068 (m-30) REVERT: C 363 GLU cc_start: 0.7579 (tt0) cc_final: 0.6761 (tp30) REVERT: C 550 GLN cc_start: 0.8357 (pt0) cc_final: 0.8066 (pt0) REVERT: C 578 MET cc_start: 0.7862 (ttt) cc_final: 0.7411 (tpp) REVERT: C 612 LYS cc_start: 0.7816 (mmtm) cc_final: 0.7341 (tttp) REVERT: C 705 LEU cc_start: 0.9071 (mp) cc_final: 0.8844 (mp) REVERT: C 713 MET cc_start: 0.8114 (mmt) cc_final: 0.7704 (mmp) REVERT: C 734 LYS cc_start: 0.8957 (tppp) cc_final: 0.8581 (tppt) REVERT: D 219 ARG cc_start: 0.8462 (mmt90) cc_final: 0.7843 (mmt90) REVERT: D 278 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7143 (tm-30) REVERT: D 461 ASP cc_start: 0.9030 (t70) cc_final: 0.8672 (t70) REVERT: D 551 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8537 (mm) REVERT: D 625 MET cc_start: 0.8151 (ttp) cc_final: 0.7913 (mtp) REVERT: D 730 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8578 (mmmt) REVERT: D 754 LYS cc_start: 0.8795 (mtpm) cc_final: 0.8578 (ttmm) outliers start: 93 outliers final: 60 residues processed: 482 average time/residue: 0.1184 time to fit residues: 91.5393 Evaluate side-chains 460 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 396 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 712 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN C 387 GLN C 528 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.182771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.131460 restraints weight = 33050.026| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.35 r_work: 0.3484 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 20828 Z= 0.199 Angle : 0.795 12.744 28280 Z= 0.393 Chirality : 0.045 0.281 3226 Planarity : 0.005 0.076 3512 Dihedral : 7.872 59.360 3164 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.28 % Favored : 88.28 % Rotamer: Outliers : 4.21 % Allowed : 20.02 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -1.78 (0.17), residues: 2482 helix: -0.26 (0.13), residues: 1436 sheet: -2.92 (0.50), residues: 92 loop : -2.40 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 757 TYR 0.030 0.002 TYR A 657 PHE 0.026 0.002 PHE D 284 TRP 0.014 0.002 TRP A 788 HIS 0.008 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (20824) covalent geometry : angle 0.79460 / 0.39 (28272) SS BOND : bond 0.00152 / 0.08 ( 4) SS BOND : angle 1.47941 / 0.82 ( 8) hydrogen bonds : bond 0.03540 / 2.36 ( 846) hydrogen bonds : angle 4.53693 / 3.17 ( 2490) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 411 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7313 (ttp-170) cc_final: 0.7051 (ttp-170) REVERT: A 213 LEU cc_start: 0.8214 (mm) cc_final: 0.8005 (mm) REVERT: A 234 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7910 (mm) REVERT: A 397 GLU cc_start: 0.8341 (pm20) cc_final: 0.7966 (tm-30) REVERT: A 461 ASP cc_start: 0.8580 (t70) cc_final: 0.8372 (t0) REVERT: A 734 LYS cc_start: 0.8949 (tppp) cc_final: 0.8586 (tppt) REVERT: B 182 ASP cc_start: 0.6778 (m-30) cc_final: 0.6427 (m-30) REVERT: B 278 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 287 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8781 (mp) REVERT: B 605 MET cc_start: 0.8185 (ppp) cc_final: 0.7636 (ppp) REVERT: B 612 LYS cc_start: 0.8714 (ttpm) cc_final: 0.8459 (ttpt) REVERT: B 685 MET cc_start: 0.4333 (ptt) cc_final: 0.4068 (ptm) REVERT: B 713 MET cc_start: 0.8546 (mmm) cc_final: 0.8080 (tpt) REVERT: B 782 GLU cc_start: 0.8614 (tt0) cc_final: 0.8259 (pt0) REVERT: C 219 ARG cc_start: 0.8890 (mmp80) cc_final: 0.8653 (mmp80) REVERT: C 234 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7345 (mm) REVERT: C 578 MET cc_start: 0.7930 (ttt) cc_final: 0.7458 (tpp) REVERT: C 612 LYS cc_start: 0.7865 (mmtm) cc_final: 0.7389 (tttp) REVERT: C 660 CYS cc_start: 0.4459 (OUTLIER) cc_final: 0.4247 (t) REVERT: C 705 LEU cc_start: 0.9063 (mp) cc_final: 0.8862 (mp) REVERT: C 734 LYS cc_start: 0.8978 (tppp) cc_final: 0.8642 (tppt) REVERT: D 222 ASN cc_start: 0.7407 (p0) cc_final: 0.6872 (p0) REVERT: D 278 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7275 (tm-30) REVERT: D 461 ASP cc_start: 0.9017 (t70) cc_final: 0.8615 (t70) REVERT: D 551 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8584 (mm) REVERT: D 625 MET cc_start: 0.8129 (ttp) cc_final: 0.7742 (mtm) REVERT: D 730 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8582 (mmmt) REVERT: D 754 LYS cc_start: 0.8925 (mtpm) cc_final: 0.8701 (ttmm) outliers start: 93 outliers final: 63 residues processed: 454 average time/residue: 0.1148 time to fit residues: 83.6686 Evaluate side-chains 460 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 392 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 660 CYS Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 712 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 35 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 225 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN A 267 GLN B 736 GLN C 387 GLN C 528 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.182173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.130403 restraints weight = 32997.551| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.36 r_work: 0.3467 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 20828 Z= 0.195 Angle : 0.797 12.752 28280 Z= 0.394 Chirality : 0.045 0.294 3226 Planarity : 0.005 0.084 3512 Dihedral : 7.688 57.603 3164 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.44 % Favored : 88.11 % Rotamer: Outliers : 4.62 % Allowed : 20.24 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -1.69 (0.17), residues: 2482 helix: -0.18 (0.13), residues: 1434 sheet: -2.95 (0.50), residues: 92 loop : -2.36 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 269 TYR 0.031 0.002 TYR C 657 PHE 0.027 0.002 PHE B 284 TRP 0.014 0.002 TRP A 788 HIS 0.008 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (20824) covalent geometry : angle 0.79642 / 0.39 (28272) SS BOND : bond 0.00095 / 0.04 ( 4) SS BOND : angle 1.36793 / 0.76 ( 8) hydrogen bonds : bond 0.03547 / 2.37 ( 846) hydrogen bonds : angle 4.54940 / 3.17 ( 2490) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 405 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7224 (ttp-170) cc_final: 0.6926 (ttp-170) REVERT: A 234 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7952 (mm) REVERT: A 461 ASP cc_start: 0.8605 (t70) cc_final: 0.8350 (t0) REVERT: A 734 LYS cc_start: 0.8945 (tppp) cc_final: 0.8629 (tptt) REVERT: B 182 ASP cc_start: 0.6763 (m-30) cc_final: 0.6420 (m-30) REVERT: B 278 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7346 (tm-30) REVERT: B 287 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8800 (mp) REVERT: B 482 MET cc_start: 0.8699 (mmp) cc_final: 0.8069 (mmp) REVERT: B 605 MET cc_start: 0.8248 (ppp) cc_final: 0.8002 (ppp) REVERT: B 612 LYS cc_start: 0.8718 (ttpm) cc_final: 0.8470 (ttpt) REVERT: B 625 MET cc_start: 0.7997 (ttp) cc_final: 0.7599 (ttm) REVERT: B 685 MET cc_start: 0.4090 (ptt) cc_final: 0.3854 (ptm) REVERT: B 782 GLU cc_start: 0.8620 (tt0) cc_final: 0.8265 (pt0) REVERT: C 219 ARG cc_start: 0.8943 (mmp80) cc_final: 0.8726 (mmp80) REVERT: C 234 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7236 (mm) REVERT: C 390 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8027 (tt) REVERT: C 578 MET cc_start: 0.7839 (ttt) cc_final: 0.7476 (tpp) REVERT: C 612 LYS cc_start: 0.7755 (mmtm) cc_final: 0.7131 (ttpp) REVERT: C 685 MET cc_start: 0.7395 (ptp) cc_final: 0.7057 (ptm) REVERT: C 734 LYS cc_start: 0.8979 (tppp) cc_final: 0.8648 (tppt) REVERT: D 222 ASN cc_start: 0.7329 (p0) cc_final: 0.6799 (p0) REVERT: D 278 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7324 (tm-30) REVERT: D 461 ASP cc_start: 0.9052 (t70) cc_final: 0.8708 (t70) REVERT: D 551 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8614 (mm) REVERT: D 625 MET cc_start: 0.8153 (ttp) cc_final: 0.7735 (mtm) REVERT: D 730 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8588 (mmmt) REVERT: D 754 LYS cc_start: 0.8952 (mtpm) cc_final: 0.8660 (mtmt) outliers start: 102 outliers final: 68 residues processed: 450 average time/residue: 0.1195 time to fit residues: 86.2007 Evaluate side-chains 463 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 390 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 712 ASN Chi-restraints excluded: chain D residue 768 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 188 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 75 optimal weight: 0.0970 chunk 237 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 206 optimal weight: 0.6980 chunk 233 optimal weight: 0.7980 chunk 163 optimal weight: 30.0000 chunk 60 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN A 445 ASN B 736 GLN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN C 528 ASN D 724 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.185241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134885 restraints weight = 33063.982| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.36 r_work: 0.3506 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20828 Z= 0.136 Angle : 0.783 12.992 28280 Z= 0.383 Chirality : 0.044 0.297 3226 Planarity : 0.005 0.054 3512 Dihedral : 7.500 56.112 3164 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.20 % Favored : 88.40 % Rotamer: Outliers : 4.21 % Allowed : 20.65 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: -1.53 (0.17), residues: 2482 helix: -0.03 (0.13), residues: 1432 sheet: -2.87 (0.50), residues: 92 loop : -2.32 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 269 TYR 0.030 0.001 TYR A 502 PHE 0.028 0.001 PHE B 284 TRP 0.014 0.001 TRP A 788 HIS 0.006 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (20824) covalent geometry : angle 0.78184 / 0.38 (28272) SS BOND : bond 0.00534 / 0.20 ( 4) SS BOND : angle 3.05886 / 1.58 ( 8) hydrogen bonds : bond 0.03350 / 2.23 ( 846) hydrogen bonds : angle 4.44058 / 3.09 ( 2490) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 417 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7233 (ttp-170) cc_final: 0.6897 (ttp-170) REVERT: A 228 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7450 (m-40) REVERT: A 234 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7838 (mm) REVERT: A 461 ASP cc_start: 0.8519 (t70) cc_final: 0.8249 (t0) REVERT: A 680 MET cc_start: 0.1800 (mtp) cc_final: 0.1282 (mmt) REVERT: A 685 MET cc_start: 0.8087 (tpp) cc_final: 0.7334 (ptp) REVERT: A 705 LEU cc_start: 0.9034 (mp) cc_final: 0.8748 (mp) REVERT: A 734 LYS cc_start: 0.8919 (tppp) cc_final: 0.8596 (tptt) REVERT: B 182 ASP cc_start: 0.6768 (m-30) cc_final: 0.6410 (m-30) REVERT: B 200 LEU cc_start: 0.7575 (mp) cc_final: 0.7330 (mp) REVERT: B 278 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7448 (tm-30) REVERT: B 387 GLN cc_start: 0.8619 (pt0) cc_final: 0.8415 (pt0) REVERT: B 482 MET cc_start: 0.8700 (mmp) cc_final: 0.8043 (mmp) REVERT: B 612 LYS cc_start: 0.8673 (ttpm) cc_final: 0.8407 (ttpt) REVERT: B 625 MET cc_start: 0.7896 (ttp) cc_final: 0.7522 (ttm) REVERT: B 685 MET cc_start: 0.4068 (ptt) cc_final: 0.3812 (ptm) REVERT: B 782 GLU cc_start: 0.8581 (tt0) cc_final: 0.8240 (pt0) REVERT: C 219 ARG cc_start: 0.8956 (mmp80) cc_final: 0.8721 (mmp80) REVERT: C 234 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7093 (mm) REVERT: C 271 ARG cc_start: 0.7796 (ttm110) cc_final: 0.7517 (mtm-85) REVERT: C 347 ASP cc_start: 0.8339 (m-30) cc_final: 0.8118 (m-30) REVERT: C 390 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.7912 (tt) REVERT: C 461 ASP cc_start: 0.8554 (t70) cc_final: 0.8229 (t0) REVERT: C 578 MET cc_start: 0.7730 (ttt) cc_final: 0.7484 (tpp) REVERT: C 612 LYS cc_start: 0.7694 (mmtm) cc_final: 0.7071 (ttpp) REVERT: C 685 MET cc_start: 0.7360 (ptp) cc_final: 0.7053 (ptm) REVERT: C 734 LYS cc_start: 0.8953 (tppp) cc_final: 0.8567 (tppt) REVERT: D 210 ILE cc_start: 0.8881 (mm) cc_final: 0.8582 (mt) REVERT: D 222 ASN cc_start: 0.7277 (p0) cc_final: 0.6789 (p0) REVERT: D 278 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7155 (tm-30) REVERT: D 448 GLU cc_start: 0.8632 (pt0) cc_final: 0.8367 (pm20) REVERT: D 461 ASP cc_start: 0.9049 (t70) cc_final: 0.8835 (t70) REVERT: D 517 THR cc_start: 0.8983 (m) cc_final: 0.8644 (p) REVERT: D 625 MET cc_start: 0.8081 (ttp) cc_final: 0.7686 (mtm) REVERT: D 730 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8543 (mmmt) REVERT: D 754 LYS cc_start: 0.8911 (mtpm) cc_final: 0.8685 (ttmm) outliers start: 93 outliers final: 64 residues processed: 463 average time/residue: 0.1211 time to fit residues: 88.8558 Evaluate side-chains 460 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 392 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 712 ASN Chi-restraints excluded: chain D residue 768 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 210 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 173 optimal weight: 0.0370 chunk 201 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 228 ASN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN C 528 ASN D 201 ASN D 387 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.187067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138198 restraints weight = 32728.745| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.30 r_work: 0.3561 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20828 Z= 0.134 Angle : 0.788 13.211 28280 Z= 0.385 Chirality : 0.044 0.309 3226 Planarity : 0.005 0.065 3512 Dihedral : 7.398 55.779 3164 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.88 % Favored : 88.76 % Rotamer: Outliers : 3.67 % Allowed : 21.38 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -1.45 (0.17), residues: 2482 helix: 0.05 (0.13), residues: 1428 sheet: -2.80 (0.49), residues: 92 loop : -2.31 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 757 TYR 0.036 0.002 TYR C 657 PHE 0.026 0.001 PHE B 284 TRP 0.018 0.002 TRP B 776 HIS 0.006 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (20824) covalent geometry : angle 0.78633 / 0.38 (28272) SS BOND : bond 0.00316 / 0.12 ( 4) SS BOND : angle 2.98318 / 1.67 ( 8) hydrogen bonds : bond 0.03302 / 2.21 ( 846) hydrogen bonds : angle 4.38878 / 3.06 ( 2490) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 411 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7207 (ttp-170) cc_final: 0.6938 (ttp-170) REVERT: A 202 LEU cc_start: 0.7262 (mm) cc_final: 0.7054 (mm) REVERT: A 234 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7830 (mm) REVERT: A 453 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6717 (mm-30) REVERT: A 461 ASP cc_start: 0.8487 (t70) cc_final: 0.8230 (t0) REVERT: A 685 MET cc_start: 0.7957 (tpp) cc_final: 0.7274 (ptp) REVERT: A 705 LEU cc_start: 0.9064 (mp) cc_final: 0.8768 (mp) REVERT: A 734 LYS cc_start: 0.8982 (tppp) cc_final: 0.8645 (tptt) REVERT: A 748 PHE cc_start: 0.8220 (m-10) cc_final: 0.7999 (m-10) REVERT: B 182 ASP cc_start: 0.6779 (m-30) cc_final: 0.6442 (m-30) REVERT: B 200 LEU cc_start: 0.7627 (mp) cc_final: 0.7389 (mp) REVERT: B 219 ARG cc_start: 0.8370 (mmt90) cc_final: 0.8161 (mmt90) REVERT: B 278 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7121 (tm-30) REVERT: B 482 MET cc_start: 0.8728 (mmp) cc_final: 0.8073 (mmp) REVERT: B 612 LYS cc_start: 0.8671 (ttpm) cc_final: 0.8403 (ttpt) REVERT: B 625 MET cc_start: 0.7922 (ttp) cc_final: 0.7558 (ttm) REVERT: B 685 MET cc_start: 0.4248 (ptt) cc_final: 0.3970 (ptm) REVERT: B 713 MET cc_start: 0.8372 (mmm) cc_final: 0.7987 (tpp) REVERT: B 782 GLU cc_start: 0.8579 (tt0) cc_final: 0.8287 (pt0) REVERT: C 215 ASP cc_start: 0.9323 (p0) cc_final: 0.8970 (p0) REVERT: C 219 ARG cc_start: 0.8973 (mmp80) cc_final: 0.8752 (mmp80) REVERT: C 234 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7146 (mm) REVERT: C 387 GLN cc_start: 0.8884 (tt0) cc_final: 0.8672 (tt0) REVERT: C 390 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.7847 (tt) REVERT: C 453 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6752 (mm-30) REVERT: C 461 ASP cc_start: 0.8522 (t70) cc_final: 0.8175 (t0) REVERT: C 578 MET cc_start: 0.7804 (ttt) cc_final: 0.7555 (tpp) REVERT: C 612 LYS cc_start: 0.7688 (mmtm) cc_final: 0.7069 (ttpp) REVERT: C 685 MET cc_start: 0.7278 (ptp) cc_final: 0.7001 (ptm) REVERT: D 210 ILE cc_start: 0.8900 (mm) cc_final: 0.8582 (mt) REVERT: D 222 ASN cc_start: 0.7260 (p0) cc_final: 0.6777 (p0) REVERT: D 278 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7219 (tm-30) REVERT: D 461 ASP cc_start: 0.9102 (t70) cc_final: 0.8897 (t70) REVERT: D 472 TYR cc_start: 0.8403 (m-80) cc_final: 0.8202 (m-80) REVERT: D 482 MET cc_start: 0.8248 (tpp) cc_final: 0.7882 (mmm) REVERT: D 517 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8648 (p) REVERT: D 625 MET cc_start: 0.8087 (ttp) cc_final: 0.7708 (mtm) REVERT: D 730 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8573 (mmmt) outliers start: 81 outliers final: 61 residues processed: 443 average time/residue: 0.1242 time to fit residues: 86.9037 Evaluate side-chains 457 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 392 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 712 ASN Chi-restraints excluded: chain D residue 768 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 146 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 195 optimal weight: 0.9980 chunk 236 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 chunk 3 optimal weight: 7.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 387 GLN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS C 528 ASN D 387 GLN D 731 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.180629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129242 restraints weight = 33189.686| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.34 r_work: 0.3449 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 20828 Z= 0.233 Angle : 0.853 12.749 28280 Z= 0.419 Chirality : 0.047 0.331 3226 Planarity : 0.005 0.067 3512 Dihedral : 7.537 57.085 3164 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.05 % Favored : 87.51 % Rotamer: Outliers : 3.31 % Allowed : 22.01 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -1.61 (0.17), residues: 2482 helix: -0.09 (0.13), residues: 1430 sheet: -2.93 (0.49), residues: 92 loop : -2.36 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 269 TYR 0.033 0.002 TYR C 657 PHE 0.026 0.002 PHE A 674 TRP 0.017 0.002 TRP C 733 HIS 0.012 0.002 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (20824) covalent geometry : angle 0.85181 / 0.42 (28272) SS BOND : bond 0.00280 / 0.11 ( 4) SS BOND : angle 2.30789 / 1.27 ( 8) hydrogen bonds : bond 0.03702 / 2.48 ( 846) hydrogen bonds : angle 4.58050 / 3.21 ( 2490) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 412 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7278 (ttp-170) cc_final: 0.6992 (ttp-170) REVERT: A 453 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6801 (mm-30) REVERT: A 461 ASP cc_start: 0.8601 (t70) cc_final: 0.8347 (t0) REVERT: A 685 MET cc_start: 0.8141 (tpp) cc_final: 0.7309 (ptp) REVERT: A 734 LYS cc_start: 0.8990 (tppp) cc_final: 0.8666 (tptt) REVERT: B 182 ASP cc_start: 0.6780 (m-30) cc_final: 0.6443 (m-30) REVERT: B 278 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7312 (tm-30) REVERT: B 612 LYS cc_start: 0.8701 (ttpm) cc_final: 0.8443 (ttpt) REVERT: B 625 MET cc_start: 0.7906 (ttp) cc_final: 0.7588 (ttm) REVERT: B 685 MET cc_start: 0.4078 (ptt) cc_final: 0.3836 (ptm) REVERT: B 713 MET cc_start: 0.8558 (mmm) cc_final: 0.8158 (tpt) REVERT: B 782 GLU cc_start: 0.8632 (tt0) cc_final: 0.8269 (pt0) REVERT: C 215 ASP cc_start: 0.9327 (p0) cc_final: 0.8979 (p0) REVERT: C 234 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7325 (mm) REVERT: C 390 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8230 (tt) REVERT: C 453 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6860 (mm-30) REVERT: C 461 ASP cc_start: 0.8650 (t70) cc_final: 0.8328 (t0) REVERT: C 578 MET cc_start: 0.7942 (ttt) cc_final: 0.7622 (tpp) REVERT: C 612 LYS cc_start: 0.7780 (mmtm) cc_final: 0.7078 (ttpp) REVERT: C 613 ASP cc_start: 0.7887 (m-30) cc_final: 0.7642 (m-30) REVERT: C 685 MET cc_start: 0.7287 (ptp) cc_final: 0.6984 (ptm) REVERT: D 222 ASN cc_start: 0.7270 (p0) cc_final: 0.6802 (p0) REVERT: D 278 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7276 (tm-30) REVERT: D 517 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8666 (p) REVERT: D 625 MET cc_start: 0.8080 (ttp) cc_final: 0.7664 (mtm) REVERT: D 730 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8591 (mmmt) REVERT: D 782 GLU cc_start: 0.8647 (tt0) cc_final: 0.8153 (pt0) outliers start: 73 outliers final: 61 residues processed: 442 average time/residue: 0.1242 time to fit residues: 86.7982 Evaluate side-chains 457 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 393 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 712 ASN Chi-restraints excluded: chain D residue 768 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 20 optimal weight: 0.6980 chunk 173 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 235 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 338 ASN B 204 ASN C 338 ASN D 387 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.185251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135288 restraints weight = 33024.942| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.34 r_work: 0.3519 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20828 Z= 0.143 Angle : 0.822 12.640 28280 Z= 0.400 Chirality : 0.045 0.328 3226 Planarity : 0.005 0.065 3512 Dihedral : 7.335 55.978 3164 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.76 % Favored : 88.80 % Rotamer: Outliers : 3.26 % Allowed : 22.92 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.17), residues: 2482 helix: 0.04 (0.13), residues: 1420 sheet: -2.86 (0.49), residues: 92 loop : -2.26 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 219 TYR 0.032 0.002 TYR C 657 PHE 0.029 0.002 PHE B 284 TRP 0.018 0.002 TRP B 776 HIS 0.027 0.001 HIS D 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (20824) covalent geometry : angle 0.82088 / 0.40 (28272) SS BOND : bond 0.00229 / 0.09 ( 4) SS BOND : angle 2.07860 / 1.13 ( 8) hydrogen bonds : bond 0.03382 / 2.27 ( 846) hydrogen bonds : angle 4.45818 / 3.12 ( 2490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4464.20 seconds wall clock time: 77 minutes 19.71 seconds (4639.71 seconds total)