Starting phenix.real_space_refine on Mon Apr 6 04:38:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4b_62052/04_2026/9k4b_62052.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4b_62052/04_2026/9k4b_62052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k4b_62052/04_2026/9k4b_62052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4b_62052/04_2026/9k4b_62052.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k4b_62052/04_2026/9k4b_62052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4b_62052/04_2026/9k4b_62052.map" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.091 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 75 5.16 5 C 9660 2.51 5 N 2574 2.21 5 O 3138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15447 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5149 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 656} Chain: "B" Number of atoms: 5149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5149 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 656} Chain: "C" Number of atoms: 5149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5149 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 656} Time building chain proxies: 3.41, per 1000 atoms: 0.22 Number of scatterers: 15447 At special positions: 0 Unit cell: (95.23, 94.16, 173.34, 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 75 16.00 O 3138 8.00 N 2574 7.00 C 9660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 748.7 milliseconds 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3684 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 27 sheets defined 7.4% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.894A pdb=" N SER A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 729 through 733 Processing helix chain 'A' and resid 762 through 764 No H-bonds generated for 'chain 'A' and resid 762 through 764' Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.890A pdb=" N SER B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 333 through 343 removed outlier: 4.228A pdb=" N THR B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 733 Processing helix chain 'B' and resid 762 through 764 No H-bonds generated for 'chain 'B' and resid 762 through 764' Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 245 through 257 removed outlier: 3.886A pdb=" N SER C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 333 through 342 Processing helix chain 'C' and resid 729 through 733 Processing helix chain 'C' and resid 762 through 764 No H-bonds generated for 'chain 'C' and resid 762 through 764' Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 280 removed outlier: 4.800A pdb=" N TYR A 293 " --> pdb=" O ARG A 321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 327 removed outlier: 6.018A pdb=" N ALA A 326 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS A 482 " --> pdb=" O CYS A 509 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 511 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 502 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS A 537 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET A 504 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASN A 539 " --> pdb=" O MET A 504 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET A 506 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS A 541 " --> pdb=" O MET A 506 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TYR A 508 " --> pdb=" O CYS A 541 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N ASN A 543 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP A 510 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N LEU A 545 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 512 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLU A 547 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 514 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 559 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 537 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 561 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 539 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR A 557 " --> pdb=" O GLY A 581 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER A 583 " --> pdb=" O TYR A 557 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A 559 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS A 580 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP A 612 " --> pdb=" O HIS A 580 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 582 " --> pdb=" O ASP A 612 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N SER A 609 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN A 636 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE A 611 " --> pdb=" O GLN A 636 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP A 633 " --> pdb=" O GLY A 656 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY A 658 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE A 635 " --> pdb=" O GLY A 658 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP A 655 " --> pdb=" O GLY A 680 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N SER A 682 " --> pdb=" O ASP A 655 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE A 657 " --> pdb=" O SER A 682 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY A 701 " --> pdb=" O ASN A 679 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS A 721 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TYR A 754 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 722 " --> pdb=" O TYR A 754 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ARG A 756 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N CYS A 724 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 362 removed outlier: 5.841A pdb=" N LEU A 360 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER A 389 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 362 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 502 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS A 537 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET A 504 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASN A 539 " --> pdb=" O MET A 504 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET A 506 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS A 541 " --> pdb=" O MET A 506 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TYR A 508 " --> pdb=" O CYS A 541 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N ASN A 543 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP A 510 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N LEU A 545 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 512 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLU A 547 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 514 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU A 567 " --> pdb=" O ARG A 542 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU A 566 " --> pdb=" O GLY A 595 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LEU A 597 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 568 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ASN A 599 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A 570 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 620 " --> pdb=" O GLY A 595 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU A 597 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A 622 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 599 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 642 " --> pdb=" O ARG A 667 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE A 669 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR A 644 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR A 666 " --> pdb=" O ASN A 689 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLU A 691 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A 668 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 398 removed outlier: 10.501A pdb=" N THR A 394 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 11.876A pdb=" N ASP A 479 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 396 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR A 424 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 443 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR A 458 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE A 452 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN A 456 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 490 through 491 removed outlier: 6.221A pdb=" N PHE A 491 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 519 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA A 551 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE A 575 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER A 603 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA A 627 " --> pdb=" O ASP A 650 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA A 649 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 810 through 814 removed outlier: 6.516A pdb=" N THR A 881 " --> pdb=" O ILE A 849 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 823 removed outlier: 6.636A pdb=" N SER A 868 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 863 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR A 870 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 829 through 830 Processing sheet with id=AB1, first strand: chain 'B' and resid 277 through 280 removed outlier: 4.802A pdb=" N TYR B 293 " --> pdb=" O ARG B 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 326 through 327 removed outlier: 6.007A pdb=" N ALA B 326 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS B 482 " --> pdb=" O CYS B 509 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN B 511 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 502 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LYS B 537 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET B 504 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASN B 539 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N MET B 506 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N CYS B 541 " --> pdb=" O MET B 506 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TYR B 508 " --> pdb=" O CYS B 541 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N ASN B 543 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP B 510 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N LEU B 545 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE B 512 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLU B 547 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 514 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL B 559 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS B 537 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE B 561 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 539 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR B 557 " --> pdb=" O GLY B 581 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER B 583 " --> pdb=" O TYR B 557 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 559 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS B 580 " --> pdb=" O GLY B 610 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASP B 612 " --> pdb=" O HIS B 580 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 582 " --> pdb=" O ASP B 612 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER B 609 " --> pdb=" O GLY B 634 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN B 636 " --> pdb=" O SER B 609 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE B 611 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP B 633 " --> pdb=" O GLY B 656 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B 658 " --> pdb=" O ASP B 633 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE B 635 " --> pdb=" O GLY B 658 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP B 655 " --> pdb=" O GLY B 680 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER B 682 " --> pdb=" O ASP B 655 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE B 657 " --> pdb=" O SER B 682 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 701 " --> pdb=" O ASN B 679 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS B 721 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR B 754 " --> pdb=" O ALA B 720 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 722 " --> pdb=" O TYR B 754 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ARG B 756 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N CYS B 724 " --> pdb=" O ARG B 756 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 360 through 362 removed outlier: 5.847A pdb=" N LEU B 360 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N SER B 389 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 362 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 502 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LYS B 537 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET B 504 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASN B 539 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N MET B 506 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N CYS B 541 " --> pdb=" O MET B 506 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TYR B 508 " --> pdb=" O CYS B 541 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N ASN B 543 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP B 510 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N LEU B 545 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE B 512 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLU B 547 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 514 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU B 567 " --> pdb=" O ARG B 542 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU B 566 " --> pdb=" O GLY B 595 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N LEU B 597 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN B 599 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL B 570 " --> pdb=" O ASN B 599 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE B 620 " --> pdb=" O GLY B 595 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 597 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE B 622 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B 599 " --> pdb=" O PHE B 622 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 642 " --> pdb=" O ARG B 667 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE B 669 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR B 644 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR B 666 " --> pdb=" O ASN B 689 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU B 691 " --> pdb=" O THR B 666 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU B 668 " --> pdb=" O GLU B 691 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 354 through 356 Processing sheet with id=AB5, first strand: chain 'B' and resid 391 through 399 removed outlier: 10.505A pdb=" N THR B 394 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N ASP B 479 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 396 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR B 424 " --> pdb=" O MET B 478 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 443 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR B 458 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE B 452 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN B 456 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 490 through 491 removed outlier: 6.273A pdb=" N PHE B 491 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 519 " --> pdb=" O TYR B 552 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 551 " --> pdb=" O ASP B 576 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE B 575 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER B 603 " --> pdb=" O TYR B 628 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA B 627 " --> pdb=" O ASP B 650 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA B 649 " --> pdb=" O THR B 674 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 810 through 814 removed outlier: 6.506A pdb=" N THR B 881 " --> pdb=" O ILE B 849 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 819 through 823 removed outlier: 6.635A pdb=" N SER B 868 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 863 " --> pdb=" O SER B 868 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR B 870 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 829 through 830 Processing sheet with id=AC1, first strand: chain 'C' and resid 277 through 280 removed outlier: 4.801A pdb=" N TYR C 293 " --> pdb=" O ARG C 321 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 326 through 327 removed outlier: 6.020A pdb=" N ALA C 326 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS C 482 " --> pdb=" O CYS C 509 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN C 511 " --> pdb=" O LYS C 482 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N MET C 504 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASN C 539 " --> pdb=" O MET C 504 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N MET C 506 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N CYS C 541 " --> pdb=" O MET C 506 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYR C 508 " --> pdb=" O CYS C 541 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ASN C 543 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP C 510 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N LEU C 545 " --> pdb=" O ASP C 510 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 512 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLU C 547 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 514 " --> pdb=" O GLU C 547 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 559 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS C 537 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE C 561 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASN C 539 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR C 557 " --> pdb=" O GLY C 581 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER C 583 " --> pdb=" O TYR C 557 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL C 559 " --> pdb=" O SER C 583 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N HIS C 580 " --> pdb=" O GLY C 610 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASP C 612 " --> pdb=" O HIS C 580 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL C 582 " --> pdb=" O ASP C 612 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N SER C 609 " --> pdb=" O GLY C 634 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN C 636 " --> pdb=" O SER C 609 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE C 611 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY C 656 " --> pdb=" O ASP C 633 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP C 655 " --> pdb=" O GLY C 680 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N SER C 682 " --> pdb=" O ASP C 655 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE C 657 " --> pdb=" O SER C 682 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY C 701 " --> pdb=" O ASN C 679 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS C 721 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR C 754 " --> pdb=" O ALA C 720 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 722 " --> pdb=" O TYR C 754 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ARG C 756 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N CYS C 724 " --> pdb=" O ARG C 756 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 360 through 362 removed outlier: 5.858A pdb=" N LEU C 360 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER C 389 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 362 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N MET C 504 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASN C 539 " --> pdb=" O MET C 504 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N MET C 506 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N CYS C 541 " --> pdb=" O MET C 506 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYR C 508 " --> pdb=" O CYS C 541 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ASN C 543 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP C 510 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N LEU C 545 " --> pdb=" O ASP C 510 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 512 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLU C 547 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 514 " --> pdb=" O GLU C 547 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU C 567 " --> pdb=" O ARG C 542 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU C 566 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LEU C 597 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C 568 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASN C 599 " --> pdb=" O VAL C 568 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL C 570 " --> pdb=" O ASN C 599 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE C 620 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU C 597 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE C 622 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN C 599 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL C 642 " --> pdb=" O ARG C 667 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE C 669 " --> pdb=" O VAL C 642 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C 644 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR C 666 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU C 691 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU C 668 " --> pdb=" O GLU C 691 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AC5, first strand: chain 'C' and resid 391 through 398 removed outlier: 10.503A pdb=" N THR C 394 " --> pdb=" O ASP C 479 " (cutoff:3.500A) removed outlier: 11.893A pdb=" N ASP C 479 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE C 396 " --> pdb=" O LYS C 477 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR C 424 " --> pdb=" O MET C 478 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 443 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR C 458 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE C 452 " --> pdb=" O GLN C 456 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN C 456 " --> pdb=" O ILE C 452 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 490 through 491 removed outlier: 6.225A pdb=" N PHE C 491 " --> pdb=" O TYR C 520 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 519 " --> pdb=" O TYR C 552 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA C 551 " --> pdb=" O ASP C 576 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE C 575 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER C 603 " --> pdb=" O TYR C 628 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA C 627 " --> pdb=" O ASP C 650 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA C 649 " --> pdb=" O THR C 674 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 810 through 814 removed outlier: 6.502A pdb=" N THR C 881 " --> pdb=" O ILE C 849 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 819 through 823 removed outlier: 6.632A pdb=" N SER C 868 " --> pdb=" O ILE C 863 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE C 863 " --> pdb=" O SER C 868 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR C 870 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 829 through 830 359 hydrogen bonds defined for protein. 945 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: 3.50 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5097 1.35 - 1.48: 3987 1.48 - 1.62: 6522 1.62 - 1.75: 1 1.75 - 1.89: 98 Bond restraints: 15705 Sorted by residual: bond pdb=" N LEU C 464 " pdb=" CA LEU C 464 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.56e+00 bond pdb=" N LEU B 464 " pdb=" CA LEU B 464 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.22e+00 bond pdb=" N LEU A 464 " pdb=" CA LEU A 464 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.17e+00 bond pdb=" CG1 ILE A 512 " pdb=" CD1 ILE A 512 " ideal model delta sigma weight residual 1.513 1.417 0.096 3.90e-02 6.57e+02 6.01e+00 bond pdb=" CB CYS C 693 " pdb=" SG CYS C 693 " ideal model delta sigma weight residual 1.808 1.886 -0.078 3.30e-02 9.18e+02 5.53e+00 ... (remaining 15700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 20708 2.50 - 5.00: 574 5.00 - 7.50: 46 7.50 - 10.00: 2 10.00 - 12.50: 3 Bond angle restraints: 21333 Sorted by residual: angle pdb=" N ILE B 502 " pdb=" CA ILE B 502 " pdb=" C ILE B 502 " ideal model delta sigma weight residual 109.34 98.18 11.16 2.08e+00 2.31e-01 2.88e+01 angle pdb=" N ILE A 849 " pdb=" CA ILE A 849 " pdb=" C ILE A 849 " ideal model delta sigma weight residual 111.62 107.39 4.23 7.90e-01 1.60e+00 2.87e+01 angle pdb=" N ILE B 849 " pdb=" CA ILE B 849 " pdb=" C ILE B 849 " ideal model delta sigma weight residual 111.56 107.12 4.44 8.60e-01 1.35e+00 2.67e+01 angle pdb=" N ILE C 849 " pdb=" CA ILE C 849 " pdb=" C ILE C 849 " ideal model delta sigma weight residual 111.48 107.27 4.21 9.40e-01 1.13e+00 2.01e+01 angle pdb=" CB MET C 446 " pdb=" CG MET C 446 " pdb=" SD MET C 446 " ideal model delta sigma weight residual 112.70 100.20 12.50 3.00e+00 1.11e-01 1.74e+01 ... (remaining 21328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8562 17.98 - 35.97: 633 35.97 - 53.95: 63 53.95 - 71.94: 14 71.94 - 89.92: 10 Dihedral angle restraints: 9282 sinusoidal: 3498 harmonic: 5784 Sorted by residual: dihedral pdb=" CA TYR B 520 " pdb=" C TYR B 520 " pdb=" N GLY B 521 " pdb=" CA GLY B 521 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ILE A 886 " pdb=" C ILE A 886 " pdb=" N SER A 887 " pdb=" CA SER A 887 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASN A 717 " pdb=" C ASN A 717 " pdb=" N SER A 718 " pdb=" CA SER A 718 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 9279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1947 0.071 - 0.143: 460 0.143 - 0.214: 63 0.214 - 0.285: 10 0.285 - 0.356: 1 Chirality restraints: 2481 Sorted by residual: chirality pdb=" CB VAL B 433 " pdb=" CA VAL B 433 " pdb=" CG1 VAL B 433 " pdb=" CG2 VAL B 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA ILE B 502 " pdb=" N ILE B 502 " pdb=" C ILE B 502 " pdb=" CB ILE B 502 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB VAL A 433 " pdb=" CA VAL A 433 " pdb=" CG1 VAL A 433 " pdb=" CG2 VAL A 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2478 not shown) Planarity restraints: 2748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 586 " -0.048 2.00e-02 2.50e+03 4.57e-02 5.22e+01 pdb=" CG TRP B 586 " 0.119 2.00e-02 2.50e+03 pdb=" CD1 TRP B 586 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP B 586 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 586 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP B 586 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 586 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 586 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 586 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 586 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 586 " 0.048 2.00e-02 2.50e+03 4.54e-02 5.15e+01 pdb=" CG TRP A 586 " -0.119 2.00e-02 2.50e+03 pdb=" CD1 TRP A 586 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP A 586 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 586 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 586 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 586 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 586 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 586 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 586 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 586 " 0.049 2.00e-02 2.50e+03 4.53e-02 5.13e+01 pdb=" CG TRP C 586 " -0.119 2.00e-02 2.50e+03 pdb=" CD1 TRP C 586 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP C 586 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 586 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP C 586 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 586 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 586 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 586 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 586 " 0.005 2.00e-02 2.50e+03 ... (remaining 2745 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1295 2.74 - 3.28: 15904 3.28 - 3.82: 27577 3.82 - 4.36: 37584 4.36 - 4.90: 61100 Nonbonded interactions: 143460 Sorted by model distance: nonbonded pdb=" ND2 ASN C 778 " pdb=" OH TYR C 840 " model vdw 2.198 3.120 nonbonded pdb=" ND2 ASN B 778 " pdb=" OH TYR B 840 " model vdw 2.203 3.120 nonbonded pdb=" OD1 ASP A 273 " pdb=" NZ LYS A 316 " model vdw 2.214 3.120 nonbonded pdb=" OG SER B 522 " pdb=" N GLY B 555 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASP B 273 " pdb=" NZ LYS B 316 " model vdw 2.229 3.120 ... (remaining 143455 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.970 Find NCS groups from input model: 0.390 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:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 15705 Z= 0.365 Angle : 0.981 12.497 21333 Z= 0.564 Chirality : 0.062 0.356 2481 Planarity : 0.006 0.046 2748 Dihedral : 12.735 89.924 5598 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.15 % Favored : 95.75 % Rotamer: Outliers : 0.06 % Allowed : 2.72 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.97 (0.17), residues: 1998 helix: -1.19 (0.49), residues: 63 sheet: 0.08 (0.20), residues: 609 loop : -1.00 (0.15), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 618 TYR 0.044 0.004 TYR B 552 PHE 0.032 0.005 PHE B 734 TRP 0.119 0.007 TRP B 586 HIS 0.005 0.001 HIS C 553 Details of bonding type rmsd covalent geometry : bond 0.00753 (15705) covalent geometry : angle 0.98140 (21333) hydrogen bonds : bond 0.14901 ( 359) hydrogen bonds : angle 7.07327 ( 945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.572 Fit side-chains REVERT: A 277 GLU cc_start: 0.6381 (tt0) cc_final: 0.6060 (pt0) REVERT: A 345 ASN cc_start: 0.7796 (m-40) cc_final: 0.7499 (m-40) REVERT: A 358 LYS cc_start: 0.7669 (ptpt) cc_final: 0.7106 (pttt) REVERT: A 391 SER cc_start: 0.7721 (p) cc_final: 0.7471 (m) REVERT: A 453 ASP cc_start: 0.7065 (t0) cc_final: 0.6722 (p0) REVERT: A 524 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6449 (mp0) REVERT: A 529 ASP cc_start: 0.7560 (m-30) cc_final: 0.7247 (m-30) REVERT: A 547 GLU cc_start: 0.7019 (tt0) cc_final: 0.6539 (tm-30) REVERT: A 632 ASP cc_start: 0.7925 (t0) cc_final: 0.7702 (t0) REVERT: A 643 LYS cc_start: 0.7966 (mttp) cc_final: 0.7709 (mmmm) REVERT: A 691 GLU cc_start: 0.7680 (tt0) cc_final: 0.7406 (tt0) REVERT: A 779 LEU cc_start: 0.8509 (mt) cc_final: 0.8240 (mm) REVERT: A 796 ASN cc_start: 0.6736 (t0) cc_final: 0.6473 (t0) REVERT: A 833 SER cc_start: 0.6630 (m) cc_final: 0.6283 (p) REVERT: A 850 LEU cc_start: 0.8238 (mt) cc_final: 0.8031 (mm) REVERT: B 247 GLN cc_start: 0.6937 (tp40) cc_final: 0.6627 (tp-100) REVERT: B 277 GLU cc_start: 0.6319 (tt0) cc_final: 0.6053 (pt0) REVERT: B 358 LYS cc_start: 0.7365 (ptpt) cc_final: 0.6894 (pttt) REVERT: B 391 SER cc_start: 0.7565 (p) cc_final: 0.7361 (m) REVERT: B 418 LYS cc_start: 0.7316 (mttt) cc_final: 0.6766 (pttt) REVERT: B 453 ASP cc_start: 0.7366 (t0) cc_final: 0.7012 (p0) REVERT: B 506 MET cc_start: 0.8101 (mmp) cc_final: 0.7840 (mmm) REVERT: B 547 GLU cc_start: 0.7327 (tt0) cc_final: 0.6801 (tm-30) REVERT: B 618 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7697 (mtt-85) REVERT: B 632 ASP cc_start: 0.7910 (t0) cc_final: 0.7631 (t0) REVERT: B 833 SER cc_start: 0.6547 (m) cc_final: 0.6179 (p) REVERT: B 845 ASP cc_start: 0.7156 (m-30) cc_final: 0.6735 (t0) REVERT: C 277 GLU cc_start: 0.6208 (tt0) cc_final: 0.5708 (pt0) REVERT: C 358 LYS cc_start: 0.7483 (ptpt) cc_final: 0.7029 (pttp) REVERT: C 391 SER cc_start: 0.7526 (p) cc_final: 0.7321 (m) REVERT: C 418 LYS cc_start: 0.7567 (mttt) cc_final: 0.7287 (ptpt) REVERT: C 453 ASP cc_start: 0.7128 (t0) cc_final: 0.6641 (p0) REVERT: C 547 GLU cc_start: 0.7072 (tt0) cc_final: 0.6429 (tm-30) REVERT: C 632 ASP cc_start: 0.7847 (t0) cc_final: 0.7568 (t0) REVERT: C 697 ASN cc_start: 0.7734 (m-40) cc_final: 0.7478 (m-40) REVERT: C 739 ASP cc_start: 0.6982 (m-30) cc_final: 0.6703 (m-30) REVERT: C 796 ASN cc_start: 0.6648 (t0) cc_final: 0.6409 (t0) outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 0.5360 time to fit residues: 131.7785 Evaluate side-chains 146 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 502 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 ASN B 255 ASN B 797 ASN C 511 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.164854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143322 restraints weight = 13080.784| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 0.85 r_work: 0.3536 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15705 Z= 0.130 Angle : 0.554 8.196 21333 Z= 0.312 Chirality : 0.047 0.163 2481 Planarity : 0.003 0.036 2748 Dihedral : 5.661 24.363 2171 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.68 % Allowed : 5.61 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.17), residues: 1998 helix: -0.99 (0.51), residues: 93 sheet: 0.07 (0.20), residues: 630 loop : -0.79 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 667 TYR 0.021 0.001 TYR B 520 PHE 0.021 0.002 PHE B 370 TRP 0.034 0.002 TRP C 586 HIS 0.005 0.002 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00266 (15705) covalent geometry : angle 0.55360 (21333) hydrogen bonds : bond 0.04244 ( 359) hydrogen bonds : angle 5.81373 ( 945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.956 Fit side-chains REVERT: A 358 LYS cc_start: 0.7352 (ptpt) cc_final: 0.7080 (pttt) REVERT: A 524 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6782 (mp0) REVERT: A 571 ASP cc_start: 0.7631 (t0) cc_final: 0.7309 (t70) REVERT: A 833 SER cc_start: 0.6567 (m) cc_final: 0.6341 (p) REVERT: B 247 GLN cc_start: 0.6952 (tp40) cc_final: 0.6738 (tp-100) REVERT: B 358 LYS cc_start: 0.7205 (ptpt) cc_final: 0.6962 (pttp) REVERT: B 418 LYS cc_start: 0.7535 (mttt) cc_final: 0.7268 (pttt) REVERT: B 833 SER cc_start: 0.6580 (m) cc_final: 0.6310 (p) REVERT: C 358 LYS cc_start: 0.7426 (ptpt) cc_final: 0.7140 (pttt) REVERT: C 739 ASP cc_start: 0.7007 (m-30) cc_final: 0.6698 (m-30) REVERT: C 755 PHE cc_start: 0.7984 (m-80) cc_final: 0.7682 (m-80) REVERT: C 815 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7572 (mt) REVERT: C 854 ASN cc_start: 0.7061 (m110) cc_final: 0.6760 (m110) outliers start: 12 outliers final: 6 residues processed: 178 average time/residue: 0.5195 time to fit residues: 104.4394 Evaluate side-chains 137 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 815 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN B 255 ASN B 412 ASN B 796 ASN B 797 ASN C 485 ASN C 885 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138427 restraints weight = 13194.826| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 0.87 r_work: 0.3477 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15705 Z= 0.211 Angle : 0.650 7.551 21333 Z= 0.365 Chirality : 0.050 0.171 2481 Planarity : 0.004 0.038 2748 Dihedral : 6.008 27.349 2169 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 1.42 % Allowed : 7.88 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 1998 helix: -0.78 (0.51), residues: 93 sheet: -0.00 (0.21), residues: 588 loop : -0.73 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 447 TYR 0.020 0.002 TYR B 552 PHE 0.021 0.003 PHE B 370 TRP 0.028 0.002 TRP B 586 HIS 0.005 0.002 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00443 (15705) covalent geometry : angle 0.65009 (21333) hydrogen bonds : bond 0.05208 ( 359) hydrogen bonds : angle 6.01844 ( 945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 358 LYS cc_start: 0.7584 (ptpt) cc_final: 0.7190 (pttt) REVERT: A 524 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6806 (mp0) REVERT: A 571 ASP cc_start: 0.7726 (t0) cc_final: 0.7480 (t70) REVERT: A 833 SER cc_start: 0.6670 (m) cc_final: 0.6436 (p) REVERT: B 358 LYS cc_start: 0.7501 (ptpt) cc_final: 0.7145 (pttt) REVERT: B 418 LYS cc_start: 0.7710 (mttt) cc_final: 0.7317 (pttt) REVERT: C 277 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.5583 (tm-30) REVERT: C 358 LYS cc_start: 0.7443 (ptpt) cc_final: 0.7095 (pttt) REVERT: C 739 ASP cc_start: 0.7097 (m-30) cc_final: 0.6727 (m-30) REVERT: C 755 PHE cc_start: 0.8011 (m-80) cc_final: 0.7722 (m-80) REVERT: C 854 ASN cc_start: 0.7139 (m110) cc_final: 0.6939 (m-40) outliers start: 25 outliers final: 16 residues processed: 156 average time/residue: 0.4701 time to fit residues: 83.8469 Evaluate side-chains 144 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 110 optimal weight: 0.0570 chunk 134 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.164647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142910 restraints weight = 13241.196| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 0.82 r_work: 0.3537 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 1.75 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15705 Z= 0.120 Angle : 0.523 7.688 21333 Z= 0.295 Chirality : 0.046 0.157 2481 Planarity : 0.003 0.034 2748 Dihedral : 5.525 26.216 2169 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.02 % Allowed : 9.75 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 1998 helix: -0.41 (0.53), residues: 93 sheet: -0.15 (0.20), residues: 615 loop : -0.63 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 321 TYR 0.016 0.001 TYR B 520 PHE 0.015 0.002 PHE B 370 TRP 0.011 0.001 TRP B 586 HIS 0.003 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00249 (15705) covalent geometry : angle 0.52282 (21333) hydrogen bonds : bond 0.03913 ( 359) hydrogen bonds : angle 5.59970 ( 945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 358 LYS cc_start: 0.7525 (ptpt) cc_final: 0.7132 (pttt) REVERT: A 524 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6758 (mp0) REVERT: A 833 SER cc_start: 0.6730 (m) cc_final: 0.6499 (p) REVERT: B 358 LYS cc_start: 0.7444 (ptpt) cc_final: 0.6982 (pttt) REVERT: B 418 LYS cc_start: 0.7662 (mttt) cc_final: 0.7371 (pttt) REVERT: C 358 LYS cc_start: 0.7390 (ptpt) cc_final: 0.7062 (pttt) REVERT: C 739 ASP cc_start: 0.7029 (m-30) cc_final: 0.6751 (m-30) REVERT: C 755 PHE cc_start: 0.7935 (m-80) cc_final: 0.7691 (m-80) REVERT: C 854 ASN cc_start: 0.6941 (m110) cc_final: 0.6715 (m-40) outliers start: 18 outliers final: 10 residues processed: 145 average time/residue: 0.4920 time to fit residues: 81.0352 Evaluate side-chains 130 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 498 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 168 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 ASN B 247 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142296 restraints weight = 13231.133| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 0.80 r_work: 0.3528 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.3262 rms_B_bonded: 4.89 restraints_weight: 0.1250 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15705 Z= 0.139 Angle : 0.548 8.786 21333 Z= 0.306 Chirality : 0.047 0.163 2481 Planarity : 0.003 0.035 2748 Dihedral : 5.551 26.298 2169 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.81 % Allowed : 9.47 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 1998 helix: -0.36 (0.53), residues: 93 sheet: -0.22 (0.20), residues: 615 loop : -0.63 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 321 TYR 0.014 0.002 TYR B 520 PHE 0.016 0.002 PHE B 370 TRP 0.009 0.001 TRP B 586 HIS 0.002 0.001 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00291 (15705) covalent geometry : angle 0.54782 (21333) hydrogen bonds : bond 0.04080 ( 359) hydrogen bonds : angle 5.56097 ( 945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.594 Fit side-chains REVERT: A 248 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: A 257 ASN cc_start: 0.7539 (t0) cc_final: 0.7294 (t0) REVERT: A 358 LYS cc_start: 0.7772 (ptpt) cc_final: 0.7262 (pttt) REVERT: A 524 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6809 (mp0) REVERT: A 833 SER cc_start: 0.7012 (m) cc_final: 0.6723 (p) REVERT: B 358 LYS cc_start: 0.7851 (ptpt) cc_final: 0.7346 (pttt) REVERT: B 418 LYS cc_start: 0.7611 (mttt) cc_final: 0.7311 (pttt) REVERT: C 231 ASP cc_start: 0.6052 (OUTLIER) cc_final: 0.5833 (m-30) REVERT: C 277 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5850 (tm-30) REVERT: C 358 LYS cc_start: 0.7720 (ptpt) cc_final: 0.7239 (pttt) REVERT: C 739 ASP cc_start: 0.7418 (m-30) cc_final: 0.7169 (m-30) REVERT: C 755 PHE cc_start: 0.8089 (m-80) cc_final: 0.7776 (m-80) REVERT: C 854 ASN cc_start: 0.7124 (m110) cc_final: 0.6844 (m-40) outliers start: 32 outliers final: 15 residues processed: 155 average time/residue: 0.4718 time to fit residues: 83.4433 Evaluate side-chains 139 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 612 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 125 optimal weight: 0.0070 chunk 90 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 ASN B 247 GLN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.162498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139544 restraints weight = 13093.351| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 0.88 r_work: 0.3502 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15705 Z= 0.167 Angle : 0.586 8.076 21333 Z= 0.328 Chirality : 0.048 0.169 2481 Planarity : 0.003 0.040 2748 Dihedral : 5.725 26.785 2169 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.10 % Allowed : 9.69 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 1998 helix: -0.50 (0.52), residues: 93 sheet: -0.16 (0.18), residues: 756 loop : -0.73 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 447 TYR 0.015 0.002 TYR C 552 PHE 0.018 0.002 PHE B 370 TRP 0.010 0.001 TRP B 586 HIS 0.002 0.001 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00353 (15705) covalent geometry : angle 0.58579 (21333) hydrogen bonds : bond 0.04456 ( 359) hydrogen bonds : angle 5.69453 ( 945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.589 Fit side-chains REVERT: A 231 ASP cc_start: 0.6547 (OUTLIER) cc_final: 0.5899 (m-30) REVERT: A 248 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.5956 (tp30) REVERT: A 257 ASN cc_start: 0.7467 (t0) cc_final: 0.7244 (t0) REVERT: A 358 LYS cc_start: 0.7603 (ptpt) cc_final: 0.7222 (pttt) REVERT: A 524 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6888 (mp0) REVERT: A 833 SER cc_start: 0.6805 (m) cc_final: 0.6570 (p) REVERT: B 231 ASP cc_start: 0.6637 (OUTLIER) cc_final: 0.5741 (m-30) REVERT: B 358 LYS cc_start: 0.7576 (ptpt) cc_final: 0.7079 (pttt) REVERT: B 418 LYS cc_start: 0.7686 (mttt) cc_final: 0.7414 (pttt) REVERT: C 277 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5742 (tm-30) REVERT: C 358 LYS cc_start: 0.7530 (ptpt) cc_final: 0.7304 (mttt) REVERT: C 739 ASP cc_start: 0.7131 (m-30) cc_final: 0.6916 (m-30) REVERT: C 755 PHE cc_start: 0.7914 (m-80) cc_final: 0.7660 (m-80) REVERT: C 854 ASN cc_start: 0.7021 (m110) cc_final: 0.6798 (m-40) outliers start: 37 outliers final: 22 residues processed: 152 average time/residue: 0.4797 time to fit residues: 82.9715 Evaluate side-chains 145 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 552 TYR Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 830 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 114 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 0.0470 chunk 110 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 ASN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137530 restraints weight = 13062.667| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 0.85 r_work: 0.3462 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 15705 Z= 0.278 Angle : 0.732 8.200 21333 Z= 0.409 Chirality : 0.052 0.199 2481 Planarity : 0.005 0.057 2748 Dihedral : 6.231 28.970 2169 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.31 % Favored : 94.54 % Rotamer: Outliers : 2.44 % Allowed : 9.81 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 1998 helix: -0.81 (0.49), residues: 93 sheet: -0.27 (0.18), residues: 756 loop : -0.86 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 447 TYR 0.021 0.003 TYR A 552 PHE 0.022 0.003 PHE B 370 TRP 0.013 0.002 TRP B 586 HIS 0.004 0.002 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00597 (15705) covalent geometry : angle 0.73204 (21333) hydrogen bonds : bond 0.05682 ( 359) hydrogen bonds : angle 6.11410 ( 945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.608 Fit side-chains REVERT: A 358 LYS cc_start: 0.7850 (ptpt) cc_final: 0.7339 (pttt) REVERT: A 524 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7039 (mp0) REVERT: A 833 SER cc_start: 0.6770 (m) cc_final: 0.6527 (p) REVERT: B 358 LYS cc_start: 0.7728 (ptpt) cc_final: 0.7306 (pttt) REVERT: B 506 MET cc_start: 0.8662 (mmm) cc_final: 0.8455 (mmm) REVERT: C 231 ASP cc_start: 0.6610 (OUTLIER) cc_final: 0.6046 (m-30) REVERT: C 277 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5755 (tm-30) REVERT: C 358 LYS cc_start: 0.7606 (ptpt) cc_final: 0.7180 (pttt) outliers start: 43 outliers final: 26 residues processed: 156 average time/residue: 0.4935 time to fit residues: 87.5687 Evaluate side-chains 146 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 552 TYR Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 830 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 187 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 ASN B 247 GLN B 412 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142274 restraints weight = 13227.237| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 0.86 r_work: 0.3520 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15705 Z= 0.129 Angle : 0.543 8.163 21333 Z= 0.306 Chirality : 0.047 0.190 2481 Planarity : 0.003 0.038 2748 Dihedral : 5.659 26.650 2169 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.59 % Allowed : 10.88 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 1998 helix: -0.58 (0.52), residues: 93 sheet: -0.25 (0.18), residues: 753 loop : -0.77 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 321 TYR 0.016 0.001 TYR B 520 PHE 0.017 0.002 PHE B 370 TRP 0.006 0.001 TRP C 884 HIS 0.003 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00271 (15705) covalent geometry : angle 0.54292 (21333) hydrogen bonds : bond 0.04077 ( 359) hydrogen bonds : angle 5.64442 ( 945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.599 Fit side-chains REVERT: A 358 LYS cc_start: 0.7718 (ptpt) cc_final: 0.7238 (pttt) REVERT: A 524 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6892 (mp0) REVERT: A 833 SER cc_start: 0.6826 (m) cc_final: 0.6586 (p) REVERT: B 231 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.5770 (m-30) REVERT: B 358 LYS cc_start: 0.7634 (ptpt) cc_final: 0.7180 (pttt) REVERT: B 418 LYS cc_start: 0.7726 (mttt) cc_final: 0.7228 (pttt) REVERT: C 358 LYS cc_start: 0.7537 (ptpt) cc_final: 0.7205 (mttt) REVERT: C 437 ASN cc_start: 0.6722 (t0) cc_final: 0.6478 (t0) REVERT: C 854 ASN cc_start: 0.7066 (m110) cc_final: 0.6847 (m-40) outliers start: 28 outliers final: 16 residues processed: 147 average time/residue: 0.5021 time to fit residues: 83.9055 Evaluate side-chains 137 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 612 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 117 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 162 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.163335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141400 restraints weight = 13074.619| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 0.85 r_work: 0.3501 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15705 Z= 0.139 Angle : 0.551 8.581 21333 Z= 0.310 Chirality : 0.047 0.185 2481 Planarity : 0.003 0.040 2748 Dihedral : 5.616 26.747 2169 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.42 % Allowed : 11.00 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.89 (0.18), residues: 1998 helix: -0.53 (0.52), residues: 93 sheet: -0.18 (0.19), residues: 732 loop : -0.83 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 321 TYR 0.014 0.002 TYR B 520 PHE 0.017 0.002 PHE B 370 TRP 0.006 0.001 TRP B 586 HIS 0.003 0.001 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00293 (15705) covalent geometry : angle 0.55061 (21333) hydrogen bonds : bond 0.04123 ( 359) hydrogen bonds : angle 5.58564 ( 945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.599 Fit side-chains REVERT: A 231 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6110 (m-30) REVERT: A 266 ASP cc_start: 0.7079 (m-30) cc_final: 0.6677 (m-30) REVERT: A 358 LYS cc_start: 0.7757 (ptpt) cc_final: 0.7298 (pttt) REVERT: A 524 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6890 (mp0) REVERT: A 833 SER cc_start: 0.6841 (m) cc_final: 0.6604 (p) REVERT: B 231 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.5726 (m-30) REVERT: B 358 LYS cc_start: 0.7685 (ptpt) cc_final: 0.7206 (pttt) REVERT: B 418 LYS cc_start: 0.7730 (mttt) cc_final: 0.7254 (pttt) REVERT: C 231 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6112 (m-30) REVERT: C 358 LYS cc_start: 0.7581 (ptpt) cc_final: 0.7253 (mttt) REVERT: C 437 ASN cc_start: 0.6739 (t0) cc_final: 0.6390 (t0) outliers start: 25 outliers final: 18 residues processed: 143 average time/residue: 0.5113 time to fit residues: 82.8193 Evaluate side-chains 145 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 612 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 37 optimal weight: 8.9990 chunk 119 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 136 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 247 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.164310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142412 restraints weight = 13187.269| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 0.85 r_work: 0.3513 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15705 Z= 0.130 Angle : 0.536 8.524 21333 Z= 0.302 Chirality : 0.047 0.188 2481 Planarity : 0.003 0.039 2748 Dihedral : 5.530 26.704 2169 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.30 % Allowed : 11.11 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.85 (0.18), residues: 1998 helix: -0.46 (0.52), residues: 93 sheet: -0.16 (0.19), residues: 732 loop : -0.80 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 321 TYR 0.017 0.001 TYR C 552 PHE 0.016 0.002 PHE B 370 TRP 0.006 0.001 TRP C 884 HIS 0.002 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00272 (15705) covalent geometry : angle 0.53592 (21333) hydrogen bonds : bond 0.03937 ( 359) hydrogen bonds : angle 5.52677 ( 945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.630 Fit side-chains REVERT: A 231 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6110 (m-30) REVERT: A 266 ASP cc_start: 0.7073 (m-30) cc_final: 0.6680 (m-30) REVERT: A 358 LYS cc_start: 0.7731 (ptpt) cc_final: 0.7284 (pttt) REVERT: A 833 SER cc_start: 0.6841 (m) cc_final: 0.6608 (p) REVERT: B 231 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.5722 (m-30) REVERT: B 358 LYS cc_start: 0.7659 (ptpt) cc_final: 0.7181 (pttt) REVERT: B 418 LYS cc_start: 0.7725 (mttt) cc_final: 0.7263 (pttt) REVERT: C 231 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6048 (m-30) REVERT: C 358 LYS cc_start: 0.7537 (ptpt) cc_final: 0.7240 (mttt) REVERT: C 437 ASN cc_start: 0.6580 (t0) cc_final: 0.6190 (t0) REVERT: C 854 ASN cc_start: 0.7063 (m110) cc_final: 0.6855 (m-40) outliers start: 23 outliers final: 20 residues processed: 141 average time/residue: 0.5124 time to fit residues: 81.9768 Evaluate side-chains 148 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 612 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 134 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 796 ASN B 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.159394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.136956 restraints weight = 13032.092| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 0.93 r_work: 0.3444 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 15705 Z= 0.295 Angle : 0.747 8.936 21333 Z= 0.418 Chirality : 0.053 0.216 2481 Planarity : 0.005 0.058 2748 Dihedral : 6.250 29.000 2169 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 1.76 % Allowed : 10.71 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.17), residues: 1998 helix: -0.83 (0.49), residues: 93 sheet: -0.16 (0.20), residues: 624 loop : -0.91 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 447 TYR 0.025 0.003 TYR C 552 PHE 0.021 0.003 PHE B 370 TRP 0.010 0.002 TRP B 586 HIS 0.005 0.002 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00635 (15705) covalent geometry : angle 0.74699 (21333) hydrogen bonds : bond 0.05748 ( 359) hydrogen bonds : angle 6.11908 ( 945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6058.30 seconds wall clock time: 104 minutes 9.51 seconds (6249.51 seconds total)