Starting phenix.real_space_refine on Thu Sep 18 19:16:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sjl_10218/09_2025/6sjl_10218.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sjl_10218/09_2025/6sjl_10218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sjl_10218/09_2025/6sjl_10218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sjl_10218/09_2025/6sjl_10218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sjl_10218/09_2025/6sjl_10218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sjl_10218/09_2025/6sjl_10218.map" } resolution = 2.6 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= 1.000 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 96 5.16 5 C 12174 2.51 5 N 3455 2.21 5 O 3734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19459 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2376 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 10, 'TRANS': 313} Chain breaks: 1 Chain: "B" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2376 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 10, 'TRANS': 313} Chain breaks: 1 Chain: "C" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2376 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 10, 'TRANS': 313} Chain breaks: 1 Chain: "D" Number of atoms: 4105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4105 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 22, 'TRANS': 498} Chain breaks: 2 Chain: "E" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4113 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 22, 'TRANS': 499} Chain breaks: 2 Chain: "F" Number of atoms: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4113 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 22, 'TRANS': 499} Chain breaks: 2 Time building chain proxies: 4.79, per 1000 atoms: 0.25 Number of scatterers: 19459 At special positions: 0 Unit cell: (149.504, 154.624, 136.192, 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 96 16.00 O 3734 8.00 N 3455 7.00 C 12174 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: 1.63 Conformation dependent library (CDL) restraints added in 820.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4594 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 28 sheets defined 28.9% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 577 through 601 Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.718A pdb=" N GLN A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'B' and resid 567 through 571 Processing helix chain 'B' and resid 577 through 601 Processing helix chain 'B' and resid 607 through 619 removed outlier: 3.821A pdb=" N GLN B 611 " --> pdb=" O ASP B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 622 No H-bonds generated for 'chain 'B' and resid 620 through 622' Processing helix chain 'C' and resid 567 through 571 Processing helix chain 'C' and resid 577 through 601 Processing helix chain 'C' and resid 607 through 619 removed outlier: 3.711A pdb=" N GLN C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing helix chain 'D' and resid 52 through 58 Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 71 through 84 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.544A pdb=" N SER D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 179 Processing helix chain 'D' and resid 198 through 212 Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.601A pdb=" N ALA D 218 " --> pdb=" O ASP D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 315 removed outlier: 3.509A pdb=" N ILE D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 348 Processing helix chain 'D' and resid 349 through 365 Processing helix chain 'D' and resid 366 through 369 Processing helix chain 'D' and resid 371 through 375 removed outlier: 3.534A pdb=" N HIS D 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 394 removed outlier: 3.513A pdb=" N ALA D 394 " --> pdb=" O ASN D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 431 Processing helix chain 'D' and resid 442 through 446 removed outlier: 3.818A pdb=" N GLN D 446 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 451 through 467 Processing helix chain 'D' and resid 475 through 483 Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.539A pdb=" N ILE D 533 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 59 removed outlier: 3.817A pdb=" N LYS E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.535A pdb=" N ILE E 85 " --> pdb=" O PHE E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 109 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 155 through 178 Processing helix chain 'E' and resid 198 through 212 Processing helix chain 'E' and resid 214 through 226 removed outlier: 3.546A pdb=" N ALA E 218 " --> pdb=" O ASP E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 315 Processing helix chain 'E' and resid 345 through 348 Processing helix chain 'E' and resid 349 through 365 Processing helix chain 'E' and resid 366 through 369 Processing helix chain 'E' and resid 371 through 375 Processing helix chain 'E' and resid 388 through 394 Processing helix chain 'E' and resid 416 through 431 Processing helix chain 'E' and resid 442 through 446 removed outlier: 3.998A pdb=" N GLN E 446 " --> pdb=" O THR E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 451 through 467 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.559A pdb=" N LYS E 484 " --> pdb=" O TYR E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.743A pdb=" N ILE E 533 " --> pdb=" O ASP E 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 59 removed outlier: 3.822A pdb=" N LYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 86 removed outlier: 3.510A pdb=" N ILE F 85 " --> pdb=" O PHE F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 109 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 155 through 179 Processing helix chain 'F' and resid 198 through 212 Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.502A pdb=" N ALA F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 315 Processing helix chain 'F' and resid 345 through 348 Processing helix chain 'F' and resid 349 through 365 Processing helix chain 'F' and resid 366 through 369 Processing helix chain 'F' and resid 371 through 375 Processing helix chain 'F' and resid 388 through 394 Processing helix chain 'F' and resid 416 through 431 Processing helix chain 'F' and resid 442 through 446 removed outlier: 3.693A pdb=" N GLN F 446 " --> pdb=" O THR F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 451 through 467 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.778A pdb=" N LYS F 484 " --> pdb=" O TYR F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.523A pdb=" N ILE F 533 " --> pdb=" O ASP F 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 9.898A pdb=" N TRP B 551 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU A 542 " --> pdb=" O TRP B 551 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER B 553 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA A 544 " --> pdb=" O SER B 553 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ARG B 555 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 546 " --> pdb=" O ARG B 555 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 552 " --> pdb=" O PHE C 561 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N SER C 563 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE B 554 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 560 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N HIS C 629 " --> pdb=" O ILE C 560 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE C 562 " --> pdb=" O HIS C 629 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY A 635 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 642 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N MET C 654 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 644 " --> pdb=" O MET C 654 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN A 685 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N SER C 679 " --> pdb=" O GLN A 685 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 687 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N MET A 684 " --> pdb=" O ASN B 694 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLN B 696 " --> pdb=" O MET A 684 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 686 " --> pdb=" O GLN B 696 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP A 711 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N SER C 706 " --> pdb=" O ASP A 711 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN A 713 " --> pdb=" O SER C 706 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 710 " --> pdb=" O THR B 720 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER B 722 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 712 " --> pdb=" O SER B 722 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 493 through 497 removed outlier: 6.712A pdb=" N GLN C 526 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU C 546 " --> pdb=" O GLN C 526 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN C 528 " --> pdb=" O ALA C 544 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 544 " --> pdb=" O ASN C 528 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY C 530 " --> pdb=" O GLU C 542 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU C 542 " --> pdb=" O GLY C 530 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN C 532 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 552 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER B 563 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE A 554 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE B 560 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N HIS B 629 " --> pdb=" O ILE B 560 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 562 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG A 643 " --> pdb=" O MET C 636 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N SER C 638 " --> pdb=" O ARG A 643 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA A 645 " --> pdb=" O SER C 638 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE A 667 " --> pdb=" O SER B 676 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU B 678 " --> pdb=" O PHE A 667 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 669 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL B 675 " --> pdb=" O GLN C 685 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU C 687 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 677 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 693 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N SER B 705 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 695 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR A 720 " --> pdb=" O ILE C 712 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER C 714 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER A 722 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 719 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA B 730 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 721 " --> pdb=" O ALA B 730 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 743 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS C 754 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 745 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 493 through 497 removed outlier: 6.791A pdb=" N GLN B 526 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 546 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN B 528 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA B 544 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY B 530 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU B 542 " --> pdb=" O GLY B 530 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B 532 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N TRP C 551 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU B 542 " --> pdb=" O TRP C 551 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER C 553 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 544 " --> pdb=" O SER C 553 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ARG C 555 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 546 " --> pdb=" O ARG C 555 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY A 559 " --> pdb=" O ILE C 552 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE C 554 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE A 561 " --> pdb=" O ILE C 554 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY C 556 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER A 563 " --> pdb=" O GLY C 556 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 560 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N HIS A 629 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 562 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 651 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR B 662 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 653 " --> pdb=" O THR B 662 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET B 684 " --> pdb=" O ASN C 694 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLN C 696 " --> pdb=" O MET B 684 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 686 " --> pdb=" O GLN C 696 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU A 726 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL C 721 " --> pdb=" O GLU A 726 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 728 " --> pdb=" O VAL C 721 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA C 723 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 730 " --> pdb=" O ALA C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 783 through 784 Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 9 removed outlier: 4.322A pdb=" N TYR D 4 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP D 8 " --> pdb=" O LYS D 28 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS D 28 " --> pdb=" O ASP D 8 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N CYS D 185 " --> pdb=" O PRO D 31 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG D 33 " --> pdb=" O CYS D 185 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA D 187 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL D 35 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D 189 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 37 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE D 191 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE D 39 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL D 193 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE D 41 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY D 195 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE D 43 " --> pdb=" O GLY D 195 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N GLU D 237 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE D 189 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG D 239 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE D 191 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU D 241 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL D 193 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU D 243 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY D 195 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N LEU D 304 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN D 281 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU D 306 " --> pdb=" O GLN D 281 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N THR D 283 " --> pdb=" O LEU D 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 805 through 809 removed outlier: 3.501A pdb=" N VAL A 829 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 799 " --> pdb=" O VAL A 827 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 783 through 784 removed outlier: 3.807A pdb=" N ALA E 27 " --> pdb=" O THR B 784 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 4 through 9 removed outlier: 4.307A pdb=" N TYR E 4 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE E 184 " --> pdb=" O PRO E 31 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG E 33 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE E 186 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL E 35 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS E 188 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N GLU E 237 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE E 189 " --> pdb=" O GLU E 237 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG E 239 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE E 191 " --> pdb=" O ARG E 239 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU E 241 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL E 193 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU E 243 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY E 195 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU E 304 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN E 281 " --> pdb=" O LEU E 304 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU E 306 " --> pdb=" O GLN E 281 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THR E 283 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 805 through 809 removed outlier: 3.620A pdb=" N VAL B 829 " --> pdb=" O ARG B 797 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 783 through 785 removed outlier: 3.673A pdb=" N ALA F 27 " --> pdb=" O THR C 784 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 9 removed outlier: 4.252A pdb=" N TYR F 4 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS F 28 " --> pdb=" O ASP F 8 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N CYS F 185 " --> pdb=" O PRO F 31 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG F 33 " --> pdb=" O CYS F 185 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ALA F 187 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL F 35 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE F 189 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU F 37 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE F 191 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE F 39 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL F 193 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE F 41 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLY F 195 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE F 43 " --> pdb=" O GLY F 195 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N GLU F 237 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE F 189 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG F 239 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE F 191 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU F 241 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL F 193 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU F 243 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY F 195 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N LYS F 278 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG F 239 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE F 280 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU F 241 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE F 282 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU F 243 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ALA F 284 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU F 304 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN F 281 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU F 306 " --> pdb=" O GLN F 281 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR F 283 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 795 through 799 Processing sheet with id=AB4, first strand: chain 'C' and resid 826 through 827 removed outlier: 3.545A pdb=" N HIS F 14 " --> pdb=" O VAL C 826 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 294 through 295 removed outlier: 6.345A pdb=" N LEU D 294 " --> pdb=" O TRP D 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 328 through 331 Processing sheet with id=AB7, first strand: chain 'D' and resid 328 through 331 removed outlier: 4.419A pdb=" N GLN D 398 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 495 through 497 Processing sheet with id=AB9, first strand: chain 'D' and resid 500 through 502 Processing sheet with id=AC1, first strand: chain 'E' and resid 294 through 295 removed outlier: 6.431A pdb=" N LEU E 294 " --> pdb=" O TRP E 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 328 through 331 removed outlier: 3.595A pdb=" N GLU E 336 " --> pdb=" O ALA E 403 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 328 through 331 removed outlier: 4.421A pdb=" N GLN E 398 " --> pdb=" O VAL E 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 495 through 497 Processing sheet with id=AC5, first strand: chain 'E' and resid 500 through 502 Processing sheet with id=AC6, first strand: chain 'F' and resid 294 through 295 removed outlier: 6.310A pdb=" N LEU F 294 " --> pdb=" O TRP F 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 328 through 331 Processing sheet with id=AC8, first strand: chain 'F' and resid 328 through 331 removed outlier: 4.599A pdb=" N GLN F 398 " --> pdb=" O VAL F 386 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 495 through 497 Processing sheet with id=AD1, first strand: chain 'F' and resid 500 through 502 810 hydrogen bonds defined for protein. 2250 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: 4.37 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4813 1.32 - 1.44: 3715 1.44 - 1.57: 11096 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 19789 Sorted by residual: bond pdb=" CB ARG B 547 " pdb=" CG ARG B 547 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.09e+00 bond pdb=" CB ARG A 547 " pdb=" CG ARG A 547 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.12e+00 bond pdb=" C SER D 197 " pdb=" N ARG D 198 " ideal model delta sigma weight residual 1.333 1.299 0.034 1.41e-02 5.03e+03 5.93e+00 bond pdb=" CG ARG B 547 " pdb=" CD ARG B 547 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.84e+00 bond pdb=" C SER E 197 " pdb=" N ARG E 198 " ideal model delta sigma weight residual 1.333 1.299 0.034 1.41e-02 5.03e+03 5.77e+00 ... (remaining 19784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 26353 2.95 - 5.89: 342 5.89 - 8.84: 17 8.84 - 11.78: 0 11.78 - 14.73: 1 Bond angle restraints: 26713 Sorted by residual: angle pdb=" C ALA F 411 " pdb=" N VAL F 412 " pdb=" CA VAL F 412 " ideal model delta sigma weight residual 122.59 119.08 3.51 7.20e-01 1.93e+00 2.38e+01 angle pdb=" C GLU B 812 " pdb=" N ASN B 813 " pdb=" CA ASN B 813 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N ARG D 198 " pdb=" CA ARG D 198 " pdb=" C ARG D 198 " ideal model delta sigma weight residual 114.75 109.19 5.56 1.26e+00 6.30e-01 1.95e+01 angle pdb=" N ARG E 198 " pdb=" CA ARG E 198 " pdb=" C ARG E 198 " ideal model delta sigma weight residual 114.75 109.35 5.40 1.26e+00 6.30e-01 1.83e+01 angle pdb=" C LYS E 29 " pdb=" N LYS E 30 " pdb=" CA LYS E 30 " ideal model delta sigma weight residual 121.59 136.32 -14.73 3.54e+00 7.98e-02 1.73e+01 ... (remaining 26708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10764 17.96 - 35.93: 943 35.93 - 53.89: 182 53.89 - 71.85: 46 71.85 - 89.81: 12 Dihedral angle restraints: 11947 sinusoidal: 4777 harmonic: 7170 Sorted by residual: dihedral pdb=" CA ASP A 811 " pdb=" C ASP A 811 " pdb=" N GLU A 812 " pdb=" CA GLU A 812 " ideal model delta harmonic sigma weight residual 180.00 147.36 32.64 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA VAL D 24 " pdb=" C VAL D 24 " pdb=" N VAL D 25 " pdb=" CA VAL D 25 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ARG D 198 " pdb=" C ARG D 198 " pdb=" N GLY D 199 " pdb=" CA GLY D 199 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 11944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2276 0.064 - 0.128: 625 0.128 - 0.193: 59 0.193 - 0.257: 0 0.257 - 0.321: 2 Chirality restraints: 2962 Sorted by residual: chirality pdb=" CG LEU A 783 " pdb=" CB LEU A 783 " pdb=" CD1 LEU A 783 " pdb=" CD2 LEU A 783 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE C 823 " pdb=" CA ILE C 823 " pdb=" CG1 ILE C 823 " pdb=" CG2 ILE C 823 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU A 642 " pdb=" CB LEU A 642 " pdb=" CD1 LEU A 642 " pdb=" CD2 LEU A 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 2959 not shown) Planarity restraints: 3524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 81 " 0.029 2.00e-02 2.50e+03 2.99e-02 1.56e+01 pdb=" CG PHE E 81 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE E 81 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE E 81 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 81 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 81 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE E 81 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 81 " 0.032 2.00e-02 2.50e+03 2.95e-02 1.53e+01 pdb=" CG PHE F 81 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE F 81 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE F 81 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 81 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 81 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE F 81 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 81 " -0.026 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE D 81 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE D 81 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE D 81 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 81 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 81 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 81 " -0.002 2.00e-02 2.50e+03 ... (remaining 3521 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 216 2.57 - 3.15: 16243 3.15 - 3.73: 31551 3.73 - 4.32: 49900 4.32 - 4.90: 79453 Nonbonded interactions: 177363 Sorted by model distance: nonbonded pdb=" NH2 ARG D 422 " pdb=" O LEU D 445 " model vdw 1.985 3.120 nonbonded pdb=" NH2 ARG E 422 " pdb=" O LEU E 445 " model vdw 2.050 3.120 nonbonded pdb=" NH2 ARG F 422 " pdb=" O LEU F 445 " model vdw 2.050 3.120 nonbonded pdb=" O ARG A 640 " pdb=" OG SER B 646 " model vdw 2.088 3.040 nonbonded pdb=" O ARG B 640 " pdb=" OG SER C 646 " model vdw 2.110 3.040 ... (remaining 177358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 3 through 133 or resid 143 through 539)) selection = (chain 'F' and (resid 3 through 133 or resid 143 through 539)) } 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.930 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:8.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.013 0.124 19789 Z= 0.572 Angle : 0.866 14.729 26713 Z= 0.481 Chirality : 0.055 0.321 2962 Planarity : 0.005 0.045 3524 Dihedral : 14.603 89.815 7353 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.74 % Favored : 94.06 % Rotamer: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -2.82 (0.14), residues: 2507 helix: -1.54 (0.17), residues: 621 sheet: -1.80 (0.22), residues: 418 loop : -2.08 (0.14), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 547 TYR 0.018 0.003 TYR D 4 PHE 0.068 0.004 PHE E 81 TRP 0.020 0.003 TRP D 501 HIS 0.009 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.01309 (19789) covalent geometry : angle 0.86597 (26713) hydrogen bonds : bond 0.17376 ( 798) hydrogen bonds : angle 7.56151 ( 2250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.795 Fit side-chains REVERT: B 596 LYS cc_start: 0.8399 (mtmt) cc_final: 0.8194 (mttt) REVERT: D 4 TYR cc_start: 0.7191 (m-80) cc_final: 0.6857 (m-80) REVERT: D 170 GLN cc_start: 0.7376 (tt0) cc_final: 0.7073 (tt0) REVERT: E 3 LYS cc_start: 0.7782 (mmpt) cc_final: 0.7456 (tttm) REVERT: E 5 GLN cc_start: 0.6938 (pp30) cc_final: 0.6652 (pp30) REVERT: E 50 ARG cc_start: 0.7578 (mtt90) cc_final: 0.7364 (mtm110) REVERT: E 67 ARG cc_start: 0.8682 (mmm160) cc_final: 0.8454 (mmt-90) REVERT: E 73 LYS cc_start: 0.7915 (mppt) cc_final: 0.7657 (mppt) REVERT: E 167 ARG cc_start: 0.7448 (mmt90) cc_final: 0.7233 (mmm160) REVERT: E 170 GLN cc_start: 0.7176 (tm-30) cc_final: 0.6973 (tt0) REVERT: E 338 GLU cc_start: 0.8275 (pt0) cc_final: 0.7934 (pt0) REVERT: E 348 ASP cc_start: 0.7264 (m-30) cc_final: 0.7038 (m-30) REVERT: E 352 TYR cc_start: 0.8519 (t80) cc_final: 0.8271 (t80) REVERT: E 410 MET cc_start: 0.8364 (mmm) cc_final: 0.8157 (mmm) REVERT: F 167 ARG cc_start: 0.7240 (mmt90) cc_final: 0.7013 (mmm160) REVERT: F 333 SER cc_start: 0.8323 (t) cc_final: 0.7916 (p) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.8695 time to fit residues: 253.2919 Evaluate side-chains 190 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN A 514 HIS A 583 GLN A 605 GLN A 694 ASN A 696 GLN B 502 ASN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS B 567 GLN B 583 GLN B 615 ASN B 725 GLN B 791 GLN C 502 ASN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 GLN C 571 GLN C 583 GLN C 615 ASN C 813 ASN D 49 ASN D 76 GLN D 179 ASN D 190 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN D 213 GLN D 295 ASN D 370 HIS D 487 HIS D 493 ASN D 512 HIS E 14 HIS E 76 GLN E 179 ASN E 190 GLN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN E 213 GLN E 281 GLN E 286 ASN E 370 HIS E 429 GLN E 442 ASN E 472 GLN E 487 HIS E 493 ASN E 512 HIS F 20 ASN F 76 GLN F 170 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 GLN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 213 GLN F 281 GLN F 286 ASN F 487 HIS F 493 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.157046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098453 restraints weight = 19467.201| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.54 r_work: 0.3098 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19789 Z= 0.175 Angle : 0.598 8.145 26713 Z= 0.326 Chirality : 0.045 0.230 2962 Planarity : 0.004 0.048 3524 Dihedral : 6.156 29.453 2711 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.41 % Allowed : 10.52 % Favored : 87.07 % 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 aren not related in a simple way. whole: -1.66 (0.16), residues: 2507 helix: 0.14 (0.19), residues: 633 sheet: -1.37 (0.21), residues: 452 loop : -1.61 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 33 TYR 0.011 0.001 TYR E 7 PHE 0.022 0.002 PHE D 43 TRP 0.015 0.001 TRP F 22 HIS 0.005 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00369 (19789) covalent geometry : angle 0.59778 (26713) hydrogen bonds : bond 0.04421 ( 798) hydrogen bonds : angle 5.35453 ( 2250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 249 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7909 (ttt-90) REVERT: A 571 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: A 704 MET cc_start: 0.8945 (ttp) cc_final: 0.8585 (ttp) REVERT: B 596 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8244 (mttt) REVERT: C 615 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8813 (t0) REVERT: D 170 GLN cc_start: 0.7383 (tt0) cc_final: 0.7119 (tt0) REVERT: D 226 ARG cc_start: 0.6926 (mtp85) cc_final: 0.6724 (mtp85) REVERT: E 3 LYS cc_start: 0.7618 (mmpt) cc_final: 0.7259 (tttm) REVERT: E 50 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7404 (mtm110) REVERT: E 73 LYS cc_start: 0.7892 (mppt) cc_final: 0.7653 (mppt) REVERT: E 167 ARG cc_start: 0.7551 (mmt90) cc_final: 0.7250 (mmm160) REVERT: E 170 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7091 (tt0) REVERT: E 228 ASP cc_start: 0.7790 (m-30) cc_final: 0.7371 (m-30) REVERT: E 272 ARG cc_start: 0.7169 (mmp-170) cc_final: 0.6923 (mmt-90) REVERT: E 338 GLU cc_start: 0.8160 (pt0) cc_final: 0.7664 (pt0) REVERT: E 346 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: E 347 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7724 (mtm) REVERT: E 348 ASP cc_start: 0.7290 (m-30) cc_final: 0.6931 (m-30) REVERT: E 363 MET cc_start: 0.8318 (mtt) cc_final: 0.8034 (mtt) REVERT: E 389 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8045 (m) REVERT: E 410 MET cc_start: 0.8573 (mmm) cc_final: 0.8309 (mmm) REVERT: E 439 ARG cc_start: 0.7041 (mpp-170) cc_final: 0.6487 (mmt180) REVERT: E 453 PHE cc_start: 0.8096 (t80) cc_final: 0.7776 (m-10) REVERT: F 144 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6832 (mmm) REVERT: F 167 ARG cc_start: 0.7163 (mmt90) cc_final: 0.6829 (mmm160) REVERT: F 333 SER cc_start: 0.8498 (t) cc_final: 0.8192 (p) REVERT: F 346 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7555 (mt-10) REVERT: F 348 ASP cc_start: 0.7725 (t70) cc_final: 0.7499 (t0) REVERT: F 370 HIS cc_start: 0.7621 (m-70) cc_final: 0.7343 (m90) outliers start: 50 outliers final: 10 residues processed: 276 average time/residue: 0.7737 time to fit residues: 234.6780 Evaluate side-chains 219 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 346 GLU Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 92 optimal weight: 0.0000 chunk 107 optimal weight: 3.9990 chunk 250 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 GLN A 707 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN B 725 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 ASN C 725 GLN D 49 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 ASN E 472 GLN E 512 HIS ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.155354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097554 restraints weight = 20274.500| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.69 r_work: 0.3209 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19789 Z= 0.192 Angle : 0.585 7.801 26713 Z= 0.316 Chirality : 0.045 0.218 2962 Planarity : 0.004 0.041 3524 Dihedral : 5.938 30.430 2711 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.36 % Allowed : 12.64 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.25 (0.16), residues: 2507 helix: 0.79 (0.20), residues: 635 sheet: -1.25 (0.22), residues: 452 loop : -1.47 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 353 TYR 0.012 0.001 TYR A 796 PHE 0.024 0.002 PHE E 43 TRP 0.011 0.001 TRP F 22 HIS 0.005 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00425 (19789) covalent geometry : angle 0.58519 (26713) hydrogen bonds : bond 0.04151 ( 798) hydrogen bonds : angle 5.11963 ( 2250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7630 (ttt-90) REVERT: A 571 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: B 596 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7927 (mtmt) REVERT: B 640 ARG cc_start: 0.8630 (mtt180) cc_final: 0.8414 (mtt-85) REVERT: B 750 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8280 (pp30) REVERT: D 22 TRP cc_start: 0.5409 (OUTLIER) cc_final: 0.4998 (m100) REVERT: D 170 GLN cc_start: 0.7022 (tt0) cc_final: 0.6745 (tt0) REVERT: D 348 ASP cc_start: 0.7584 (t70) cc_final: 0.6844 (t0) REVERT: E 3 LYS cc_start: 0.7670 (mmpt) cc_final: 0.7179 (tttm) REVERT: E 50 ARG cc_start: 0.7531 (mtt90) cc_final: 0.6930 (mtm110) REVERT: E 73 LYS cc_start: 0.7475 (mppt) cc_final: 0.7080 (mppt) REVERT: E 167 ARG cc_start: 0.7063 (mmt90) cc_final: 0.6650 (mmm160) REVERT: E 170 GLN cc_start: 0.6992 (tm-30) cc_final: 0.6742 (tt0) REVERT: E 228 ASP cc_start: 0.7641 (m-30) cc_final: 0.7116 (m-30) REVERT: E 272 ARG cc_start: 0.6678 (mmp-170) cc_final: 0.6450 (mmt180) REVERT: E 338 GLU cc_start: 0.8116 (pt0) cc_final: 0.7412 (pt0) REVERT: E 346 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: E 347 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7685 (mmm) REVERT: E 348 ASP cc_start: 0.7302 (m-30) cc_final: 0.6796 (m-30) REVERT: E 363 MET cc_start: 0.8060 (mtt) cc_final: 0.7751 (mtt) REVERT: E 389 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7815 (m) REVERT: E 410 MET cc_start: 0.8483 (mmm) cc_final: 0.8205 (mmm) REVERT: E 439 ARG cc_start: 0.6872 (mpp-170) cc_final: 0.6213 (mmt180) REVERT: F 167 ARG cc_start: 0.6867 (mmt90) cc_final: 0.6388 (mmm160) REVERT: F 333 SER cc_start: 0.8139 (t) cc_final: 0.7732 (p) REVERT: F 346 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7424 (mt-10) REVERT: F 348 ASP cc_start: 0.7760 (t70) cc_final: 0.7322 (t0) REVERT: F 370 HIS cc_start: 0.7236 (m-70) cc_final: 0.6932 (m90) outliers start: 49 outliers final: 21 residues processed: 244 average time/residue: 0.7501 time to fit residues: 203.1300 Evaluate side-chains 229 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 750 GLN Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain D residue 22 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 346 GLU Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain F residue 22 TRP Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 149 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN C 514 HIS C 725 GLN D 49 ASN D 123 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS E 387 ASN E 512 HIS ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.092396 restraints weight = 19750.642| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.49 r_work: 0.3008 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 19789 Z= 0.306 Angle : 0.645 7.679 26713 Z= 0.346 Chirality : 0.047 0.225 2962 Planarity : 0.004 0.043 3524 Dihedral : 6.109 29.171 2711 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.38 % Allowed : 13.32 % Favored : 83.30 % 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 aren not related in a simple way. whole: -1.18 (0.16), residues: 2507 helix: 0.78 (0.20), residues: 645 sheet: -1.17 (0.21), residues: 481 loop : -1.42 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 547 TYR 0.014 0.002 TYR A 796 PHE 0.021 0.002 PHE F 81 TRP 0.012 0.002 TRP D 501 HIS 0.007 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00693 (19789) covalent geometry : angle 0.64470 (26713) hydrogen bonds : bond 0.04477 ( 798) hydrogen bonds : angle 5.20905 ( 2250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 202 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: B 507 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8588 (tp30) REVERT: B 596 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8137 (mttt) REVERT: D 22 TRP cc_start: 0.5538 (OUTLIER) cc_final: 0.5067 (m100) REVERT: D 24 VAL cc_start: 0.6617 (OUTLIER) cc_final: 0.5950 (m) REVERT: D 170 GLN cc_start: 0.7239 (tt0) cc_final: 0.6952 (tt0) REVERT: D 348 ASP cc_start: 0.7526 (t70) cc_final: 0.6806 (t0) REVERT: D 477 GLU cc_start: 0.6867 (pp20) cc_final: 0.6361 (pm20) REVERT: E 3 LYS cc_start: 0.7757 (mmpt) cc_final: 0.7171 (tttm) REVERT: E 50 ARG cc_start: 0.7738 (mtt90) cc_final: 0.7157 (mtm110) REVERT: E 167 ARG cc_start: 0.7341 (mmt90) cc_final: 0.6942 (mmm160) REVERT: E 170 GLN cc_start: 0.7300 (tm-30) cc_final: 0.6976 (tt0) REVERT: E 228 ASP cc_start: 0.7706 (m-30) cc_final: 0.7215 (m-30) REVERT: E 272 ARG cc_start: 0.6904 (mmp-170) cc_final: 0.6688 (mmt180) REVERT: E 338 GLU cc_start: 0.8179 (pt0) cc_final: 0.7525 (pt0) REVERT: E 346 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: E 347 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7528 (mtm) REVERT: E 348 ASP cc_start: 0.7350 (m-30) cc_final: 0.6869 (m-30) REVERT: E 363 MET cc_start: 0.8085 (mtt) cc_final: 0.7758 (mtt) REVERT: E 389 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.8040 (m) REVERT: E 410 MET cc_start: 0.8583 (mmm) cc_final: 0.8343 (mmm) REVERT: E 439 ARG cc_start: 0.6967 (mpp-170) cc_final: 0.6389 (mmt180) REVERT: E 453 PHE cc_start: 0.7977 (t80) cc_final: 0.7625 (m-10) REVERT: E 469 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: F 144 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6692 (mmm) REVERT: F 167 ARG cc_start: 0.7011 (mmt90) cc_final: 0.6448 (mmm160) REVERT: F 333 SER cc_start: 0.8339 (t) cc_final: 0.7952 (p) REVERT: F 346 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7597 (mt-10) REVERT: F 348 ASP cc_start: 0.7842 (t70) cc_final: 0.7370 (t0) REVERT: F 370 HIS cc_start: 0.7464 (m-70) cc_final: 0.7162 (m90) outliers start: 70 outliers final: 28 residues processed: 249 average time/residue: 0.6886 time to fit residues: 191.4025 Evaluate side-chains 234 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain D residue 22 TRP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 346 GLU Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain F residue 22 TRP Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 66 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 chunk 239 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN C 725 GLN D 123 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN E 512 HIS ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.156018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098354 restraints weight = 20189.763| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.68 r_work: 0.3223 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19789 Z= 0.165 Angle : 0.564 7.375 26713 Z= 0.304 Chirality : 0.045 0.281 2962 Planarity : 0.004 0.042 3524 Dihedral : 5.772 31.593 2711 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.14 % Allowed : 14.43 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.96 (0.16), residues: 2507 helix: 1.12 (0.20), residues: 647 sheet: -1.04 (0.22), residues: 452 loop : -1.38 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 353 TYR 0.016 0.001 TYR D 4 PHE 0.019 0.001 PHE D 43 TRP 0.012 0.001 TRP F 22 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00364 (19789) covalent geometry : angle 0.56388 (26713) hydrogen bonds : bond 0.03872 ( 798) hydrogen bonds : angle 4.90714 ( 2250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 212 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7764 (ttt-90) REVERT: A 571 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7905 (mm110) REVERT: A 704 MET cc_start: 0.9041 (ttp) cc_final: 0.8832 (ttp) REVERT: A 713 GLN cc_start: 0.8544 (tt0) cc_final: 0.8241 (tt0) REVERT: B 596 LYS cc_start: 0.8458 (mtmt) cc_final: 0.7980 (mtmt) REVERT: B 640 ARG cc_start: 0.8608 (mtt180) cc_final: 0.8352 (mtt-85) REVERT: B 750 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8299 (pp30) REVERT: D 22 TRP cc_start: 0.5602 (OUTLIER) cc_final: 0.5201 (m100) REVERT: D 170 GLN cc_start: 0.7043 (tt0) cc_final: 0.6755 (tt0) REVERT: D 272 ARG cc_start: 0.6464 (mmm160) cc_final: 0.6226 (mmm160) REVERT: D 348 ASP cc_start: 0.7559 (t70) cc_final: 0.6806 (t0) REVERT: D 354 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7756 (ttmm) REVERT: D 439 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.5039 (ptp90) REVERT: D 477 GLU cc_start: 0.6744 (pp20) cc_final: 0.6261 (pm20) REVERT: E 3 LYS cc_start: 0.7702 (mmpt) cc_final: 0.7100 (tttm) REVERT: E 50 ARG cc_start: 0.7520 (mtt90) cc_final: 0.6937 (mtm110) REVERT: E 73 LYS cc_start: 0.7357 (mppt) cc_final: 0.6970 (mppt) REVERT: E 167 ARG cc_start: 0.7106 (mmt90) cc_final: 0.6711 (mmm160) REVERT: E 170 GLN cc_start: 0.7152 (tm-30) cc_final: 0.6824 (tt0) REVERT: E 228 ASP cc_start: 0.7645 (m-30) cc_final: 0.7067 (m-30) REVERT: E 270 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6240 (pm20) REVERT: E 272 ARG cc_start: 0.6658 (mmp-170) cc_final: 0.6332 (mmt180) REVERT: E 300 MET cc_start: 0.7410 (tpt) cc_final: 0.7175 (tpt) REVERT: E 336 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7814 (mm-30) REVERT: E 338 GLU cc_start: 0.8081 (pt0) cc_final: 0.7460 (pt0) REVERT: E 346 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: E 347 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7711 (mmm) REVERT: E 348 ASP cc_start: 0.7291 (m-30) cc_final: 0.6773 (m-30) REVERT: E 363 MET cc_start: 0.8040 (mtt) cc_final: 0.7678 (mtt) REVERT: E 389 SER cc_start: 0.8119 (OUTLIER) cc_final: 0.7911 (m) REVERT: E 410 MET cc_start: 0.8501 (mmm) cc_final: 0.8261 (mmm) REVERT: E 439 ARG cc_start: 0.6908 (mpp-170) cc_final: 0.6244 (mmt180) REVERT: F 167 ARG cc_start: 0.6816 (mmt90) cc_final: 0.6373 (mmm160) REVERT: F 272 ARG cc_start: 0.6659 (mmm160) cc_final: 0.6222 (mmm160) REVERT: F 333 SER cc_start: 0.8227 (t) cc_final: 0.7844 (p) REVERT: F 346 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7497 (mt-10) REVERT: F 348 ASP cc_start: 0.7822 (t70) cc_final: 0.7588 (t0) REVERT: F 357 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7543 (tt0) REVERT: F 370 HIS cc_start: 0.7263 (m-70) cc_final: 0.6964 (m90) outliers start: 65 outliers final: 32 residues processed: 252 average time/residue: 0.7541 time to fit residues: 211.2427 Evaluate side-chains 246 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 796 TYR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 750 GLN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain D residue 22 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 346 GLU Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain F residue 22 TRP Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 64 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 GLN ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN C 725 GLN C 750 GLN D 49 ASN D 123 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 HIS ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.090201 restraints weight = 19632.570| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.55 r_work: 0.2998 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 19789 Z= 0.331 Angle : 0.658 7.381 26713 Z= 0.352 Chirality : 0.047 0.223 2962 Planarity : 0.004 0.042 3524 Dihedral : 6.078 28.797 2711 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.15 % Favored : 94.81 % Rotamer: Outliers : 3.47 % Allowed : 15.06 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.16), residues: 2507 helix: 0.98 (0.20), residues: 645 sheet: -1.03 (0.22), residues: 481 loop : -1.37 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 33 TYR 0.019 0.002 TYR D 4 PHE 0.019 0.002 PHE D 43 TRP 0.013 0.002 TRP D 501 HIS 0.007 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00751 (19789) covalent geometry : angle 0.65804 (26713) hydrogen bonds : bond 0.04497 ( 798) hydrogen bonds : angle 5.16913 ( 2250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 199 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8165 (mm110) REVERT: B 507 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8575 (tp30) REVERT: B 596 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8131 (mttt) REVERT: D 22 TRP cc_start: 0.5824 (OUTLIER) cc_final: 0.5391 (m100) REVERT: D 170 GLN cc_start: 0.7269 (tt0) cc_final: 0.6979 (tt0) REVERT: D 354 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8028 (ttmm) REVERT: D 439 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.5181 (ptp90) REVERT: D 477 GLU cc_start: 0.7014 (pp20) cc_final: 0.6549 (pm20) REVERT: E 3 LYS cc_start: 0.7730 (mmpt) cc_final: 0.6933 (tttm) REVERT: E 50 ARG cc_start: 0.7673 (mtt90) cc_final: 0.7127 (mtm110) REVERT: E 167 ARG cc_start: 0.7316 (mmt90) cc_final: 0.6937 (mmm160) REVERT: E 170 GLN cc_start: 0.7380 (tm-30) cc_final: 0.6999 (tt0) REVERT: E 197 SER cc_start: 0.7616 (OUTLIER) cc_final: 0.7311 (p) REVERT: E 228 ASP cc_start: 0.7682 (m-30) cc_final: 0.7159 (m-30) REVERT: E 272 ARG cc_start: 0.6825 (mmp-170) cc_final: 0.6526 (mmt180) REVERT: E 338 GLU cc_start: 0.8192 (pt0) cc_final: 0.7602 (pt0) REVERT: E 346 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: E 347 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7580 (mtm) REVERT: E 348 ASP cc_start: 0.7440 (m-30) cc_final: 0.6956 (m-30) REVERT: E 363 MET cc_start: 0.8159 (mtt) cc_final: 0.7814 (mtt) REVERT: E 389 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.8031 (m) REVERT: E 410 MET cc_start: 0.8636 (mmm) cc_final: 0.8396 (mmm) REVERT: E 439 ARG cc_start: 0.7000 (mpp-170) cc_final: 0.6398 (mmt180) REVERT: F 167 ARG cc_start: 0.7002 (mmt90) cc_final: 0.6490 (mmm160) REVERT: F 333 SER cc_start: 0.8315 (t) cc_final: 0.7946 (p) REVERT: F 346 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7645 (mt-10) REVERT: F 348 ASP cc_start: 0.8017 (t70) cc_final: 0.7765 (t0) REVERT: F 370 HIS cc_start: 0.7465 (m-70) cc_final: 0.7171 (m90) REVERT: F 539 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.5801 (ptt) outliers start: 72 outliers final: 36 residues processed: 251 average time/residue: 0.7138 time to fit residues: 199.6953 Evaluate side-chains 240 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 750 GLN Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain D residue 22 TRP Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 346 GLU Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain F residue 22 TRP Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 539 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 96 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 239 optimal weight: 0.0060 chunk 251 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN C 725 GLN C 750 GLN D 123 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.156773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099220 restraints weight = 20276.562| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.69 r_work: 0.3240 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19789 Z= 0.141 Angle : 0.553 6.887 26713 Z= 0.298 Chirality : 0.044 0.210 2962 Planarity : 0.004 0.044 3524 Dihedral : 5.657 31.003 2711 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.85 % Allowed : 16.07 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.80 (0.16), residues: 2507 helix: 1.37 (0.20), residues: 641 sheet: -0.88 (0.22), residues: 471 loop : -1.35 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 497 TYR 0.017 0.001 TYR D 4 PHE 0.016 0.001 PHE D 43 TRP 0.012 0.001 TRP F 22 HIS 0.004 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00306 (19789) covalent geometry : angle 0.55262 (26713) hydrogen bonds : bond 0.03701 ( 798) hydrogen bonds : angle 4.78232 ( 2250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7779 (ttt-90) REVERT: A 571 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7803 (mm110) REVERT: A 704 MET cc_start: 0.9027 (ttp) cc_final: 0.8807 (ttp) REVERT: A 713 GLN cc_start: 0.8557 (tt0) cc_final: 0.8247 (tt0) REVERT: B 507 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: B 596 LYS cc_start: 0.8368 (mtmt) cc_final: 0.7875 (mttt) REVERT: B 640 ARG cc_start: 0.8552 (mtt180) cc_final: 0.8269 (mtt-85) REVERT: B 750 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8253 (pp30) REVERT: D 22 TRP cc_start: 0.5767 (OUTLIER) cc_final: 0.5345 (m100) REVERT: D 170 GLN cc_start: 0.6975 (tt0) cc_final: 0.6674 (tt0) REVERT: D 272 ARG cc_start: 0.6390 (mmm160) cc_final: 0.5895 (mmp80) REVERT: D 348 ASP cc_start: 0.7585 (t70) cc_final: 0.6802 (t0) REVERT: D 354 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7755 (ttmm) REVERT: D 397 ILE cc_start: 0.8402 (mt) cc_final: 0.8043 (mm) REVERT: D 434 LEU cc_start: 0.8361 (mt) cc_final: 0.8117 (mm) REVERT: D 439 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.5131 (ptp90) REVERT: D 477 GLU cc_start: 0.6908 (pp20) cc_final: 0.6320 (pm20) REVERT: E 3 LYS cc_start: 0.7681 (mmpt) cc_final: 0.6934 (tttm) REVERT: E 50 ARG cc_start: 0.7591 (mtt90) cc_final: 0.6988 (mtm110) REVERT: E 73 LYS cc_start: 0.7291 (mppt) cc_final: 0.6921 (mppt) REVERT: E 167 ARG cc_start: 0.7033 (mmt90) cc_final: 0.6652 (mmm160) REVERT: E 170 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6733 (tt0) REVERT: E 228 ASP cc_start: 0.7606 (m-30) cc_final: 0.7053 (m-30) REVERT: E 270 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6261 (pm20) REVERT: E 300 MET cc_start: 0.7398 (tpt) cc_final: 0.7016 (tpt) REVERT: E 336 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7873 (mm-30) REVERT: E 338 GLU cc_start: 0.8084 (pt0) cc_final: 0.7418 (pt0) REVERT: E 339 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8217 (mm) REVERT: E 346 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: E 347 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7638 (mmm) REVERT: E 348 ASP cc_start: 0.7312 (m-30) cc_final: 0.6785 (m-30) REVERT: E 363 MET cc_start: 0.8003 (mtt) cc_final: 0.7645 (mtt) REVERT: E 410 MET cc_start: 0.8487 (mmm) cc_final: 0.8262 (mmm) REVERT: E 439 ARG cc_start: 0.6919 (mpp-170) cc_final: 0.6209 (mmt180) REVERT: F 59 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8381 (mtmm) REVERT: F 167 ARG cc_start: 0.6777 (mmt90) cc_final: 0.6335 (mmm160) REVERT: F 333 SER cc_start: 0.8262 (t) cc_final: 0.7830 (p) REVERT: F 346 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7446 (mt-10) REVERT: F 348 ASP cc_start: 0.7880 (t70) cc_final: 0.7611 (t0) REVERT: F 357 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7521 (tt0) REVERT: F 370 HIS cc_start: 0.7207 (m-70) cc_final: 0.6927 (m90) outliers start: 59 outliers final: 32 residues processed: 265 average time/residue: 0.7325 time to fit residues: 216.2450 Evaluate side-chains 251 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 796 TYR Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 750 GLN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 750 GLN Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain D residue 22 TRP Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 339 ILE Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 346 GLU Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain F residue 22 TRP Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 45 optimal weight: 0.6980 chunk 241 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 GLN ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN C 725 GLN D 48 ASN D 49 ASN D 123 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN E 472 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.092927 restraints weight = 19723.670| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.49 r_work: 0.3010 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19789 Z= 0.296 Angle : 0.635 6.996 26713 Z= 0.339 Chirality : 0.047 0.216 2962 Planarity : 0.004 0.048 3524 Dihedral : 5.918 28.960 2711 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.14 % Allowed : 15.97 % Favored : 80.89 % 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 aren not related in a simple way. whole: -0.87 (0.16), residues: 2507 helix: 1.16 (0.20), residues: 645 sheet: -0.91 (0.22), residues: 480 loop : -1.33 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 33 TYR 0.012 0.002 TYR F 109 PHE 0.019 0.002 PHE D 43 TRP 0.012 0.002 TRP F 22 HIS 0.006 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00672 (19789) covalent geometry : angle 0.63538 (26713) hydrogen bonds : bond 0.04283 ( 798) hydrogen bonds : angle 5.01215 ( 2250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 202 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7901 (ttt-90) REVERT: A 507 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.7770 (tp30) REVERT: A 571 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8156 (mm110) REVERT: B 507 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8582 (tp30) REVERT: B 596 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8085 (mttt) REVERT: C 750 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8392 (pp30) REVERT: D 22 TRP cc_start: 0.5833 (OUTLIER) cc_final: 0.5391 (m100) REVERT: D 170 GLN cc_start: 0.7272 (tt0) cc_final: 0.6966 (tt0) REVERT: D 348 ASP cc_start: 0.7579 (t70) cc_final: 0.6844 (t0) REVERT: D 354 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7928 (ttmm) REVERT: D 439 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.5215 (ptp90) REVERT: D 477 GLU cc_start: 0.6971 (pp20) cc_final: 0.6572 (pm20) REVERT: E 3 LYS cc_start: 0.7722 (mmpt) cc_final: 0.6913 (tttm) REVERT: E 50 ARG cc_start: 0.7650 (mtt90) cc_final: 0.7137 (mtm110) REVERT: E 73 LYS cc_start: 0.7676 (mppt) cc_final: 0.7274 (mppt) REVERT: E 167 ARG cc_start: 0.7290 (mmt90) cc_final: 0.6941 (mmm160) REVERT: E 170 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7011 (tt0) REVERT: E 228 ASP cc_start: 0.7669 (m-30) cc_final: 0.7140 (m-30) REVERT: E 270 GLU cc_start: 0.7722 (mm-30) cc_final: 0.6639 (pm20) REVERT: E 300 MET cc_start: 0.7444 (tpt) cc_final: 0.7101 (tpt) REVERT: E 338 GLU cc_start: 0.8205 (pt0) cc_final: 0.7660 (pt0) REVERT: E 347 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7578 (mtm) REVERT: E 348 ASP cc_start: 0.7435 (m-30) cc_final: 0.6951 (m-30) REVERT: E 363 MET cc_start: 0.8126 (mtt) cc_final: 0.7788 (mtt) REVERT: E 410 MET cc_start: 0.8613 (mmm) cc_final: 0.8374 (mmm) REVERT: E 439 ARG cc_start: 0.6983 (mpp-170) cc_final: 0.6374 (mmt180) REVERT: E 453 PHE cc_start: 0.7899 (t80) cc_final: 0.7593 (m-10) REVERT: F 167 ARG cc_start: 0.6988 (mmt90) cc_final: 0.6525 (mmm160) REVERT: F 333 SER cc_start: 0.8322 (t) cc_final: 0.7953 (p) REVERT: F 346 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7613 (mt-10) REVERT: F 348 ASP cc_start: 0.8035 (t70) cc_final: 0.7750 (t70) REVERT: F 370 HIS cc_start: 0.7452 (m-70) cc_final: 0.7152 (m90) outliers start: 65 outliers final: 34 residues processed: 252 average time/residue: 0.7247 time to fit residues: 203.6528 Evaluate side-chains 243 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 750 GLN Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain D residue 22 TRP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain F residue 22 TRP Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 30 optimal weight: 0.6980 chunk 192 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 GLN A 725 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN C 725 GLN C 750 GLN D 123 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098127 restraints weight = 19486.849| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.52 r_work: 0.3126 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19789 Z= 0.162 Angle : 0.566 7.148 26713 Z= 0.303 Chirality : 0.044 0.212 2962 Planarity : 0.004 0.044 3524 Dihedral : 5.662 30.090 2711 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.46 % Allowed : 16.89 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.74 (0.16), residues: 2507 helix: 1.42 (0.20), residues: 641 sheet: -0.82 (0.22), residues: 475 loop : -1.32 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 33 TYR 0.019 0.001 TYR C 521 PHE 0.019 0.001 PHE D 43 TRP 0.012 0.001 TRP F 22 HIS 0.005 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00357 (19789) covalent geometry : angle 0.56615 (26713) hydrogen bonds : bond 0.03780 ( 798) hydrogen bonds : angle 4.77093 ( 2250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8060 (ttt-90) REVERT: A 713 GLN cc_start: 0.8620 (tt0) cc_final: 0.8384 (tt0) REVERT: B 596 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8334 (mtmt) REVERT: B 750 GLN cc_start: 0.8670 (pt0) cc_final: 0.8377 (pp30) REVERT: B 831 PHE cc_start: 0.4915 (OUTLIER) cc_final: 0.4318 (t80) REVERT: C 750 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8318 (pp30) REVERT: D 22 TRP cc_start: 0.5915 (OUTLIER) cc_final: 0.5394 (m100) REVERT: D 170 GLN cc_start: 0.7513 (tt0) cc_final: 0.7220 (tt0) REVERT: D 272 ARG cc_start: 0.6754 (mmm160) cc_final: 0.6266 (mmp80) REVERT: D 338 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: D 348 ASP cc_start: 0.7430 (t70) cc_final: 0.6778 (t0) REVERT: D 354 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8048 (ttmm) REVERT: D 397 ILE cc_start: 0.8744 (mt) cc_final: 0.8403 (mm) REVERT: D 439 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.5337 (ptp90) REVERT: D 440 GLN cc_start: 0.7327 (mp10) cc_final: 0.7123 (mp10) REVERT: D 477 GLU cc_start: 0.7139 (pp20) cc_final: 0.6608 (pm20) REVERT: E 3 LYS cc_start: 0.7882 (mmpt) cc_final: 0.7167 (tttm) REVERT: E 50 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7494 (mtm110) REVERT: E 73 LYS cc_start: 0.7761 (mppt) cc_final: 0.7395 (mppt) REVERT: E 167 ARG cc_start: 0.7533 (mmt90) cc_final: 0.7262 (mmm160) REVERT: E 170 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7196 (tt0) REVERT: E 228 ASP cc_start: 0.7807 (m-30) cc_final: 0.7335 (m-30) REVERT: E 270 GLU cc_start: 0.7600 (mm-30) cc_final: 0.6716 (pm20) REVERT: E 338 GLU cc_start: 0.8172 (pt0) cc_final: 0.7657 (pt0) REVERT: E 339 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8446 (mm) REVERT: E 348 ASP cc_start: 0.7305 (m-30) cc_final: 0.6928 (m-30) REVERT: E 363 MET cc_start: 0.8258 (mtt) cc_final: 0.7950 (mtt) REVERT: E 410 MET cc_start: 0.8588 (mmm) cc_final: 0.8372 (mmm) REVERT: E 439 ARG cc_start: 0.7086 (mpp-170) cc_final: 0.6536 (mmt180) REVERT: E 453 PHE cc_start: 0.7994 (t80) cc_final: 0.7736 (m-10) REVERT: E 476 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7922 (mm-30) REVERT: F 167 ARG cc_start: 0.7075 (mmt90) cc_final: 0.6742 (mmm160) REVERT: F 333 SER cc_start: 0.8709 (t) cc_final: 0.8419 (p) REVERT: F 346 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7621 (mt-10) REVERT: F 348 ASP cc_start: 0.7930 (t70) cc_final: 0.7664 (t70) REVERT: F 357 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7748 (tt0) REVERT: F 370 HIS cc_start: 0.7651 (m-70) cc_final: 0.7396 (m90) REVERT: F 469 GLN cc_start: 0.7363 (mt0) cc_final: 0.7141 (mt0) outliers start: 51 outliers final: 32 residues processed: 250 average time/residue: 0.6682 time to fit residues: 186.0537 Evaluate side-chains 248 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 796 TYR Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 831 PHE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 750 GLN Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain D residue 22 TRP Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 339 ILE Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain F residue 22 TRP Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 99 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 231 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 GLN ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN C 725 GLN C 750 GLN D 48 ASN D 123 GLN D 190 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.151711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.093412 restraints weight = 19688.596| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.48 r_work: 0.3025 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19789 Z= 0.279 Angle : 0.634 9.260 26713 Z= 0.337 Chirality : 0.046 0.215 2962 Planarity : 0.004 0.040 3524 Dihedral : 5.860 28.864 2711 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.22 % Allowed : 17.23 % Favored : 80.55 % 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 aren not related in a simple way. whole: -0.83 (0.16), residues: 2507 helix: 1.20 (0.19), residues: 646 sheet: -0.87 (0.22), residues: 480 loop : -1.32 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 640 TYR 0.013 0.002 TYR F 290 PHE 0.019 0.002 PHE D 43 TRP 0.012 0.002 TRP F 22 HIS 0.006 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00632 (19789) covalent geometry : angle 0.63418 (26713) hydrogen bonds : bond 0.04201 ( 798) hydrogen bonds : angle 4.93868 ( 2250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7903 (ttt-90) REVERT: A 713 GLN cc_start: 0.8615 (tt0) cc_final: 0.8349 (tt0) REVERT: B 596 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8162 (mtmt) REVERT: C 750 GLN cc_start: 0.8750 (pt0) cc_final: 0.8380 (pp30) REVERT: D 22 TRP cc_start: 0.5947 (OUTLIER) cc_final: 0.5401 (m100) REVERT: D 170 GLN cc_start: 0.7269 (tt0) cc_final: 0.6960 (tt0) REVERT: D 272 ARG cc_start: 0.6540 (mmm160) cc_final: 0.6027 (mmp80) REVERT: D 338 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: D 348 ASP cc_start: 0.7619 (t70) cc_final: 0.6895 (t0) REVERT: D 354 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7886 (ttmm) REVERT: D 439 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.5191 (ptp90) REVERT: D 477 GLU cc_start: 0.6785 (pp20) cc_final: 0.6396 (pm20) REVERT: E 3 LYS cc_start: 0.7790 (mmpt) cc_final: 0.6928 (tttm) REVERT: E 50 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7222 (mtm110) REVERT: E 73 LYS cc_start: 0.7647 (mppt) cc_final: 0.7254 (mppt) REVERT: E 167 ARG cc_start: 0.7249 (mmt90) cc_final: 0.6989 (mmm160) REVERT: E 170 GLN cc_start: 0.7361 (tm-30) cc_final: 0.6823 (tt0) REVERT: E 228 ASP cc_start: 0.7664 (m-30) cc_final: 0.7135 (m-30) REVERT: E 270 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6572 (pm20) REVERT: E 338 GLU cc_start: 0.8189 (pt0) cc_final: 0.7643 (pt0) REVERT: E 348 ASP cc_start: 0.7402 (m-30) cc_final: 0.7065 (m-30) REVERT: E 410 MET cc_start: 0.8616 (mmm) cc_final: 0.8389 (mmm) REVERT: E 439 ARG cc_start: 0.6999 (mpp-170) cc_final: 0.6376 (mmt180) REVERT: E 453 PHE cc_start: 0.7896 (t80) cc_final: 0.7596 (m-10) REVERT: E 476 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7799 (mm-30) REVERT: E 539 MET cc_start: 0.6706 (ptt) cc_final: 0.6379 (ptt) REVERT: F 167 ARG cc_start: 0.6982 (mmt90) cc_final: 0.6538 (mmm160) REVERT: F 333 SER cc_start: 0.8309 (t) cc_final: 0.7946 (p) REVERT: F 346 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7690 (mt-10) REVERT: F 348 ASP cc_start: 0.7950 (t70) cc_final: 0.7649 (t70) REVERT: F 357 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7629 (tt0) REVERT: F 370 HIS cc_start: 0.7426 (m-70) cc_final: 0.7147 (m90) outliers start: 46 outliers final: 32 residues processed: 239 average time/residue: 0.6940 time to fit residues: 184.4876 Evaluate side-chains 238 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain D residue 22 TRP Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 262 ARG Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain F residue 22 TRP Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 200 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 230 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 GLN A 725 GLN ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN C 725 GLN D 190 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100499 restraints weight = 19489.194| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.56 r_work: 0.3144 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19789 Z= 0.134 Angle : 0.553 8.074 26713 Z= 0.295 Chirality : 0.044 0.210 2962 Planarity : 0.004 0.062 3524 Dihedral : 5.498 30.156 2711 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.93 % Allowed : 17.71 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.65 (0.16), residues: 2507 helix: 1.55 (0.20), residues: 642 sheet: -0.76 (0.23), residues: 471 loop : -1.30 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 640 TYR 0.013 0.001 TYR C 521 PHE 0.018 0.001 PHE D 43 TRP 0.012 0.001 TRP F 22 HIS 0.005 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00291 (19789) covalent geometry : angle 0.55319 (26713) hydrogen bonds : bond 0.03575 ( 798) hydrogen bonds : angle 4.63512 ( 2250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9329.33 seconds wall clock time: 159 minutes 8.01 seconds (9548.01 seconds total)