Starting phenix.real_space_refine on Sat Jul 4 00:07:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkr_60206/07_2026/8zkr_60206_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkr_60206/07_2026/8zkr_60206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zkr_60206/07_2026/8zkr_60206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkr_60206/07_2026/8zkr_60206.map" model { file = "/net/cci-nas-00/data/ceres_data/8zkr_60206/07_2026/8zkr_60206_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkr_60206/07_2026/8zkr_60206_trim.cif" } resolution = 2.8 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= 0.009 sd= 0.140 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 78 5.16 5 C 11114 2.51 5 N 2816 2.21 5 O 3010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17021 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5278 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 222} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 4 Unresolved chain link angles: 12 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 872 Unresolved non-hydrogen angles: 1146 Unresolved non-hydrogen dihedrals: 763 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'ARG:plan': 21, 'PHE:plan': 10, 'TYR:plan': 8, 'GLU:plan': 11, 'TRP:plan': 12, 'HIS:plan': 12, 'ASP:plan': 15, 'ASN:plan1': 7, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 527 Chain: "B" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3904 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 10, 'TRANS': 462} Chain breaks: 1 Chain: "C" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3899 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 10, 'TRANS': 461} Chain breaks: 1 Chain: "D" Number of atoms: 3798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3798 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 10, 'TRANS': 450} Chain breaks: 1 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'NAG': 2, 'PA8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.00, per 1000 atoms: 0.24 Number of scatterers: 17021 At special positions: 0 Unit cell: (127.179, 154.354, 130.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 78 16.00 P 1 15.00 O 3010 8.00 N 2816 7.00 C 11114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.04 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B1001 " - " ASN B 375 " " NAG B1002 " - " ASN B 328 " " NAG B1003 " - " ASN B 362 " " NAG C1001 " - " ASN C 362 " " NAG C1002 " - " ASN C 328 " " NAG C1003 " - " ASN C 375 " " NAG D4202 " - " ASN D 375 " " NAG D4203 " - " ASN D 328 " Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 764.6 milliseconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4134 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 6 sheets defined 59.0% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 3074 through 3102 removed outlier: 4.071A pdb=" N MET A3078 " --> pdb=" O ASN A3074 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A3088 " --> pdb=" O CYS A3084 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A3093 " --> pdb=" O MET A3089 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A3097 " --> pdb=" O ALA A3093 " (cutoff:3.500A) Processing helix chain 'A' and resid 3244 through 3249 removed outlier: 4.588A pdb=" N LEU A3249 " --> pdb=" O PHE A3245 " (cutoff:3.500A) Processing helix chain 'A' and resid 3249 through 3256 Processing helix chain 'A' and resid 3262 through 3266 removed outlier: 3.623A pdb=" N SER A3265 " --> pdb=" O ILE A3262 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A3266 " --> pdb=" O TRP A3263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3262 through 3266' Processing helix chain 'A' and resid 3278 through 3302 removed outlier: 3.777A pdb=" N CYS A3284 " --> pdb=" O ARG A3280 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A3302 " --> pdb=" O TRP A3298 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3332 Processing helix chain 'A' and resid 3334 through 3341 removed outlier: 3.913A pdb=" N LEU A3338 " --> pdb=" O TYR A3334 " (cutoff:3.500A) Processing helix chain 'A' and resid 3559 through 3577 Processing helix chain 'A' and resid 3581 through 3602 removed outlier: 3.685A pdb=" N VAL A3586 " --> pdb=" O PRO A3582 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A3588 " --> pdb=" O VAL A3584 " (cutoff:3.500A) Processing helix chain 'A' and resid 3603 through 3607 Processing helix chain 'A' and resid 3658 through 3660 No H-bonds generated for 'chain 'A' and resid 3658 through 3660' Processing helix chain 'A' and resid 3661 through 3689 removed outlier: 3.682A pdb=" N LYS A3665 " --> pdb=" O ALA A3661 " (cutoff:3.500A) Processing helix chain 'A' and resid 3691 through 3709 Processing helix chain 'A' and resid 3710 through 3716 Processing helix chain 'A' and resid 3722 through 3737 removed outlier: 5.286A pdb=" N LEU A3732 " --> pdb=" O ALA A3728 " (cutoff:3.500A) Proline residue: A3733 - end of helix Processing helix chain 'A' and resid 3828 through 3840 removed outlier: 4.410A pdb=" N ASP A3832 " --> pdb=" O GLU A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3892 through 3896 Processing helix chain 'A' and resid 3898 through 3924 Processing helix chain 'A' and resid 3933 through 3967 removed outlier: 4.771A pdb=" N LEU A3940 " --> pdb=" O TRP A3936 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A3949 " --> pdb=" O THR A3945 " (cutoff:3.500A) Processing helix chain 'A' and resid 3969 through 3973 removed outlier: 3.901A pdb=" N ARG A3972 " --> pdb=" O GLY A3969 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A3973 " --> pdb=" O ARG A3970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3969 through 3973' Processing helix chain 'A' and resid 3977 through 4005 removed outlier: 3.510A pdb=" N ALA A3981 " --> pdb=" O PHE A3977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A3982 " --> pdb=" O ASP A3978 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A3985 " --> pdb=" O ALA A3981 " (cutoff:3.500A) Processing helix chain 'A' and resid 4006 through 4009 removed outlier: 3.513A pdb=" N VAL A4009 " --> pdb=" O LEU A4006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4006 through 4009' Processing helix chain 'A' and resid 4010 through 4012 No H-bonds generated for 'chain 'A' and resid 4010 through 4012' Processing helix chain 'A' and resid 4013 through 4022 removed outlier: 3.624A pdb=" N LYS A4017 " --> pdb=" O SER A4013 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A4019 " --> pdb=" O PHE A4015 " (cutoff:3.500A) Processing helix chain 'A' and resid 4022 through 4048 removed outlier: 3.873A pdb=" N VAL A4048 " --> pdb=" O ALA A4044 " (cutoff:3.500A) Processing helix chain 'A' and resid 4056 through 4064 removed outlier: 4.568A pdb=" N LEU A4062 " --> pdb=" O VAL A4058 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A4063 " --> pdb=" O ALA A4059 " (cutoff:3.500A) Processing helix chain 'A' and resid 4066 through 4071 Processing helix chain 'A' and resid 4078 through 4083 Processing helix chain 'A' and resid 4083 through 4095 removed outlier: 3.678A pdb=" N CYS A4087 " --> pdb=" O SER A4083 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A4088 " --> pdb=" O PRO A4084 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A4089 " --> pdb=" O LEU A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4097 through 4100 Processing helix chain 'A' and resid 4101 through 4114 removed outlier: 3.749A pdb=" N ILE A4105 " --> pdb=" O LEU A4101 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A4107 " --> pdb=" O ALA A4103 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TRP A4108 " --> pdb=" O VAL A4104 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 242 Processing helix chain 'B' and resid 245 through 259 removed outlier: 4.168A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.616A pdb=" N LEU B 273 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 removed outlier: 3.516A pdb=" N PHE B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.638A pdb=" N ARG B 338 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.768A pdb=" N GLU B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.600A pdb=" N TRP B 366 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 367 " --> pdb=" O THR B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 367' Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 496 Processing helix chain 'B' and resid 506 through 530 removed outlier: 3.551A pdb=" N LEU B 510 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 541 removed outlier: 4.065A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 576 Processing helix chain 'B' and resid 580 through 620 removed outlier: 3.758A pdb=" N SER B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 642 removed outlier: 3.632A pdb=" N ILE B 640 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 653 removed outlier: 4.233A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 670 Processing helix chain 'B' and resid 671 through 695 removed outlier: 3.896A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 242 Processing helix chain 'C' and resid 246 through 259 removed outlier: 3.594A pdb=" N THR C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.678A pdb=" N LEU C 273 " --> pdb=" O PHE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 334 through 338 removed outlier: 3.677A pdb=" N ARG C 338 " --> pdb=" O GLN C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.740A pdb=" N GLU C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.611A pdb=" N TRP C 366 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 367 " --> pdb=" O THR C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 367' Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 398 through 412 removed outlier: 4.097A pdb=" N ALA C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 495 Processing helix chain 'C' and resid 501 through 505 removed outlier: 4.217A pdb=" N ARG C 504 " --> pdb=" O HIS C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 530 Processing helix chain 'C' and resid 532 through 541 removed outlier: 3.786A pdb=" N PHE C 538 " --> pdb=" O VAL C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 571 removed outlier: 3.562A pdb=" N ILE C 571 " --> pdb=" O PHE C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 576 Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.718A pdb=" N SER C 584 " --> pdb=" O ASN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 620 removed outlier: 3.544A pdb=" N LEU C 597 " --> pdb=" O CYS C 593 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 641 removed outlier: 3.648A pdb=" N ILE C 640 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 641 " --> pdb=" O PHE C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.641A pdb=" N GLU C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 671 removed outlier: 3.746A pdb=" N TYR C 660 " --> pdb=" O LEU C 656 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 671 " --> pdb=" O PHE C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 695 Processing helix chain 'D' and resid 220 through 238 removed outlier: 3.643A pdb=" N ILE D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.531A pdb=" N TYR D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.657A pdb=" N LEU D 273 " --> pdb=" O PHE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 334 through 338 Processing helix chain 'D' and resid 363 through 367 removed outlier: 3.732A pdb=" N ILE D 367 " --> pdb=" O THR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 496 removed outlier: 4.240A pdb=" N LEU D 473 " --> pdb=" O PHE D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 530 removed outlier: 3.547A pdb=" N CYS D 509 " --> pdb=" O SER D 505 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER D 530 " --> pdb=" O ILE D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 removed outlier: 3.968A pdb=" N TRP D 554 " --> pdb=" O HIS D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 572 removed outlier: 3.512A pdb=" N THR D 565 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 566 " --> pdb=" O ALA D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 583 through 620 removed outlier: 3.915A pdb=" N MET D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY D 599 " --> pdb=" O LYS D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 641 Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.652A pdb=" N ASN D 653 " --> pdb=" O ILE D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 671 removed outlier: 3.704A pdb=" N TYR D 660 " --> pdb=" O LEU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 694 removed outlier: 4.243A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3138 through 3141 removed outlier: 3.844A pdb=" N ILE A3182 " --> pdb=" O GLY A3227 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A3227 " --> pdb=" O ILE A3182 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A3184 " --> pdb=" O ALA A3225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3749 through 3751 removed outlier: 3.708A pdb=" N GLN A3751 " --> pdb=" O TYR A3819 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3857 through 3858 removed outlier: 3.640A pdb=" N LEU A3863 " --> pdb=" O SER A3858 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.563A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.585A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 391 through 394 932 hydrogen bonds defined for protein. 2703 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 2649 1.25 - 1.40: 4637 1.40 - 1.54: 9790 1.54 - 1.68: 226 1.68 - 1.83: 119 Bond restraints: 17421 Sorted by residual: bond pdb=" C ASN C 681 " pdb=" O ASN C 681 " ideal model delta sigma weight residual 1.236 1.108 0.128 1.15e-02 7.56e+03 1.24e+02 bond pdb=" C ASN B 681 " pdb=" O ASN B 681 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.19e-02 7.06e+03 4.38e+01 bond pdb=" C LEU C 535 " pdb=" O LEU C 535 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.28e-02 6.10e+03 3.35e+01 bond pdb=" CA LEU C 536 " pdb=" C LEU C 536 " ideal model delta sigma weight residual 1.524 1.455 0.069 1.26e-02 6.30e+03 3.01e+01 bond pdb=" CA GLN C 537 " pdb=" C GLN C 537 " ideal model delta sigma weight residual 1.524 1.456 0.068 1.24e-02 6.50e+03 2.99e+01 ... (remaining 17416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 23606 4.30 - 8.60: 77 8.60 - 12.90: 5 12.90 - 17.20: 5 17.20 - 21.51: 1 Bond angle restraints: 23694 Sorted by residual: angle pdb=" C ASN C 681 " pdb=" CA ASN C 681 " pdb=" CB ASN C 681 " ideal model delta sigma weight residual 110.88 89.37 21.51 1.57e+00 4.06e-01 1.88e+02 angle pdb=" N ARG A3063 " pdb=" CA ARG A3063 " pdb=" C ARG A3063 " ideal model delta sigma weight residual 112.58 126.85 -14.27 1.22e+00 6.72e-01 1.37e+02 angle pdb=" N ALA A3306 " pdb=" CA ALA A3306 " pdb=" C ALA A3306 " ideal model delta sigma weight residual 112.54 98.22 14.32 1.51e+00 4.39e-01 8.99e+01 angle pdb=" C TRP A3806 " pdb=" CA TRP A3806 " pdb=" CB TRP A3806 " ideal model delta sigma weight residual 115.79 104.72 11.07 1.19e+00 7.06e-01 8.65e+01 angle pdb=" N TRP A3806 " pdb=" CA TRP A3806 " pdb=" C TRP A3806 " ideal model delta sigma weight residual 109.32 125.43 -16.11 1.84e+00 2.95e-01 7.66e+01 ... (remaining 23689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.37: 9690 23.37 - 46.75: 454 46.75 - 70.12: 39 70.12 - 93.50: 13 93.50 - 116.87: 3 Dihedral angle restraints: 10199 sinusoidal: 3810 harmonic: 6389 Sorted by residual: dihedral pdb=" C ASN C 681 " pdb=" N ASN C 681 " pdb=" CA ASN C 681 " pdb=" CB ASN C 681 " ideal model delta harmonic sigma weight residual -122.60 -98.91 -23.69 0 2.50e+00 1.60e-01 8.98e+01 dihedral pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " pdb=" SG CYS C 344 " pdb=" CB CYS C 344 " ideal model delta sinusoidal sigma weight residual 93.00 171.98 -78.98 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " pdb=" CB CYS B 344 " ideal model delta sinusoidal sigma weight residual 93.00 46.98 46.02 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 10196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2714 0.122 - 0.244: 22 0.244 - 0.366: 4 0.366 - 0.488: 2 0.488 - 0.610: 1 Chirality restraints: 2743 Sorted by residual: chirality pdb=" CA ARG A3063 " pdb=" N ARG A3063 " pdb=" C ARG A3063 " pdb=" CB ARG A3063 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.31e+00 chirality pdb=" C1 NAG D4203 " pdb=" ND2 ASN D 328 " pdb=" C2 NAG D4203 " pdb=" O5 NAG D4203 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA TRP A3806 " pdb=" N TRP A3806 " pdb=" C TRP A3806 " pdb=" CB TRP A3806 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 2740 not shown) Planarity restraints: 2969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A3806 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C TRP A3806 " -0.059 2.00e-02 2.50e+03 pdb=" O TRP A3806 " 0.023 2.00e-02 2.50e+03 pdb=" N SER A3807 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A3298 " 0.019 2.00e-02 2.50e+03 2.12e-02 1.13e+01 pdb=" CG TRP A3298 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A3298 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A3298 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A3298 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A3298 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A3298 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A3298 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A3298 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A3298 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 681 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C ASN C 681 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN C 681 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP C 682 " -0.015 2.00e-02 2.50e+03 ... (remaining 2966 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 41 2.43 - 3.05: 11209 3.05 - 3.67: 24216 3.67 - 4.28: 35470 4.28 - 4.90: 60006 Nonbonded interactions: 130942 Sorted by model distance: nonbonded pdb=" OE1 GLN C 542 " pdb=" OE2 GLU D 340 " model vdw 1.813 3.040 nonbonded pdb=" OG SER B 263 " pdb=" OE1 GLU B 266 " model vdw 2.083 3.040 nonbonded pdb=" OG SER D 505 " pdb=" OD1 ASN D 508 " model vdw 2.143 3.040 nonbonded pdb=" OH TYR D 386 " pdb=" OE1 GLU D 444 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.223 3.040 ... (remaining 130937 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 'B' and (resid 219 through 293 or resid 313 through 698 or resid 1002 thr \ ough 1003)) selection = (chain 'C' and (resid 219 through 293 or resid 313 through 698 or resid 1002 thr \ ough 1003)) selection = (chain 'D' and (resid 219 through 698 or resid 4202 through 4203)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.890 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.005 0.128 17432 Z= 0.268 Angle : 0.752 21.506 23724 Z= 0.435 Chirality : 0.047 0.610 2743 Planarity : 0.004 0.042 2961 Dihedral : 13.287 116.871 6056 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.07 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2160 helix: 0.76 (0.16), residues: 1136 sheet: -0.42 (0.40), residues: 188 loop : -2.80 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 251 TYR 0.017 0.001 TYR D 249 PHE 0.035 0.001 PHE A3291 TRP 0.057 0.001 TRP A3298 HIS 0.013 0.001 HIS A3559 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.27 (17421) covalent geometry : angle 0.74498 / 0.43 (23694) SS BOND : bond 0.00344 / 0.17 ( 3) SS BOND : angle 3.36331 / 2.69 ( 6) hydrogen bonds : bond 0.15143 / 11.15 ( 932) hydrogen bonds : angle 6.01221 / 4.28 ( 2703) link_NAG-ASN : bond 0.00703 / 0.68 ( 8) link_NAG-ASN : angle 2.79324 / 1.74 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 3246 ARG cc_start: 0.4501 (tmm160) cc_final: 0.3811 (mpp80) REVERT: A 3262 ILE cc_start: 0.7445 (tp) cc_final: 0.7239 (tt) REVERT: A 3274 ARG cc_start: 0.3882 (mtt180) cc_final: 0.3086 (mtp85) REVERT: A 3923 HIS cc_start: 0.6607 (t-170) cc_final: 0.5798 (t70) REVERT: A 3933 LEU cc_start: 0.6368 (mt) cc_final: 0.6142 (mm) REVERT: B 456 GLN cc_start: 0.7820 (tt0) cc_final: 0.7119 (tt0) REVERT: B 490 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7151 (tt0) REVERT: B 603 MET cc_start: 0.6698 (mtp) cc_final: 0.6490 (mtp) REVERT: B 643 ASP cc_start: 0.7801 (t0) cc_final: 0.7446 (t0) REVERT: C 267 LYS cc_start: 0.8224 (mmtt) cc_final: 0.8012 (pmtt) REVERT: C 353 GLU cc_start: 0.8455 (pt0) cc_final: 0.8218 (pt0) REVERT: C 456 GLN cc_start: 0.7787 (tt0) cc_final: 0.7267 (tp40) REVERT: C 577 ILE cc_start: 0.8282 (pt) cc_final: 0.7943 (pp) REVERT: C 622 GLN cc_start: 0.7774 (mm110) cc_final: 0.7505 (mm-40) REVERT: C 643 ASP cc_start: 0.7664 (t0) cc_final: 0.7307 (t0) REVERT: C 675 MET cc_start: 0.7173 (mtp) cc_final: 0.6920 (mtt) REVERT: D 248 TYR cc_start: 0.6770 (t80) cc_final: 0.6504 (m-80) REVERT: D 259 ASP cc_start: 0.7230 (p0) cc_final: 0.6965 (OUTLIER) REVERT: D 342 LYS cc_start: 0.7701 (mttt) cc_final: 0.7318 (mtpp) REVERT: D 380 TRP cc_start: 0.6505 (t-100) cc_final: 0.5803 (m-90) REVERT: D 556 ILE cc_start: 0.8031 (mt) cc_final: 0.7778 (OUTLIER) REVERT: D 590 MET cc_start: 0.7463 (mmm) cc_final: 0.6959 (mmm) outliers start: 0 outliers final: 2 residues processed: 306 average time/residue: 0.5173 time to fit residues: 178.6477 Evaluate side-chains 200 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 30.0000 chunk 212 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3295 ASN B 681 ASN C 255 GLN C 508 ASN C 585 GLN C 613 GLN C 681 ASN D 508 ASN D 580 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.189046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129378 restraints weight = 20170.123| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.22 r_work: 0.3265 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17432 Z= 0.223 Angle : 0.672 9.675 23724 Z= 0.358 Chirality : 0.046 0.341 2743 Planarity : 0.005 0.065 2961 Dihedral : 5.874 53.625 2550 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.29 % Favored : 91.67 % Rotamer: Outliers : 2.74 % Allowed : 9.23 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.18), residues: 2160 helix: 0.92 (0.15), residues: 1161 sheet: -0.53 (0.39), residues: 186 loop : -2.90 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A3662 TYR 0.018 0.002 TYR C 348 PHE 0.025 0.002 PHE A3680 TRP 0.014 0.002 TRP A3298 HIS 0.010 0.001 HIS D 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.22 (17421) covalent geometry : angle 0.66463 / 0.36 (23694) SS BOND : bond 0.00376 / 0.18 ( 3) SS BOND : angle 2.61103 / 1.97 ( 6) hydrogen bonds : bond 0.06579 / 4.87 ( 932) hydrogen bonds : angle 4.62284 / 3.31 ( 2703) link_NAG-ASN : bond 0.00234 / 0.19 ( 8) link_NAG-ASN : angle 2.96072 / 1.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.667 Fit side-chains TARDY: cannot create tardy model for: "HIS A3061 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 3246 ARG cc_start: 0.4737 (tmm160) cc_final: 0.3931 (tpp80) REVERT: A 3274 ARG cc_start: 0.4354 (mtt180) cc_final: 0.3386 (mtp85) REVERT: A 3678 MET cc_start: 0.8581 (tpt) cc_final: 0.8187 (tpt) REVERT: A 3923 HIS cc_start: 0.6764 (t-170) cc_final: 0.5829 (t70) REVERT: A 3933 LEU cc_start: 0.6421 (mt) cc_final: 0.6165 (mm) REVERT: B 456 GLN cc_start: 0.8439 (tt0) cc_final: 0.7860 (tt0) REVERT: B 490 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7385 (tt0) REVERT: B 643 ASP cc_start: 0.8352 (t0) cc_final: 0.8003 (t0) REVERT: C 267 LYS cc_start: 0.8475 (mmtt) cc_final: 0.7939 (pmtt) REVERT: C 306 ARG cc_start: 0.8222 (mpp-170) cc_final: 0.7925 (mpp-170) REVERT: C 456 GLN cc_start: 0.8549 (tt0) cc_final: 0.8080 (tt0) REVERT: C 536 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7829 (mt) REVERT: C 577 ILE cc_start: 0.8412 (pt) cc_final: 0.8056 (pp) REVERT: C 622 GLN cc_start: 0.8495 (mm110) cc_final: 0.8219 (mm-40) REVERT: C 644 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7044 (pp) REVERT: C 675 MET cc_start: 0.8343 (mtp) cc_final: 0.8048 (mtt) REVERT: D 234 LEU cc_start: 0.7385 (tt) cc_final: 0.7108 (tt) REVERT: D 248 TYR cc_start: 0.7319 (t80) cc_final: 0.6869 (m-80) REVERT: D 259 ASP cc_start: 0.7501 (p0) cc_final: 0.7163 (OUTLIER) REVERT: D 342 LYS cc_start: 0.7801 (mttt) cc_final: 0.7283 (mtpp) REVERT: D 380 TRP cc_start: 0.7130 (t-100) cc_final: 0.6298 (m-90) REVERT: D 416 ASP cc_start: 0.8543 (m-30) cc_final: 0.8180 (m-30) REVERT: D 522 ILE cc_start: 0.7499 (mm) cc_final: 0.7240 (OUTLIER) REVERT: D 590 MET cc_start: 0.8258 (mmm) cc_final: 0.7951 (mmm) outliers start: 46 outliers final: 25 residues processed: 255 average time/residue: 0.5576 time to fit residues: 160.2990 Evaluate side-chains 236 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3286 LEU Chi-restraints excluded: chain A residue 3290 LEU Chi-restraints excluded: chain A residue 3325 VAL Chi-restraints excluded: chain A residue 3328 VAL Chi-restraints excluded: chain A residue 3341 LEU Chi-restraints excluded: chain A residue 3591 SER Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 4020 CYS Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3559 HIS C 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.192137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133196 restraints weight = 20354.246| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.23 r_work: 0.3322 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17432 Z= 0.121 Angle : 0.558 12.238 23724 Z= 0.295 Chirality : 0.041 0.329 2743 Planarity : 0.004 0.049 2961 Dihedral : 5.379 58.485 2550 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.92 % Favored : 92.04 % Rotamer: Outliers : 2.80 % Allowed : 10.89 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 2160 helix: 1.32 (0.16), residues: 1149 sheet: -0.40 (0.39), residues: 186 loop : -2.72 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3662 TYR 0.013 0.001 TYR C 348 PHE 0.025 0.001 PHE D 480 TRP 0.011 0.001 TRP D 293 HIS 0.006 0.001 HIS A3559 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (17421) covalent geometry : angle 0.55052 / 0.29 (23694) SS BOND : bond 0.00107 / 0.05 ( 3) SS BOND : angle 2.48225 / 1.65 ( 6) hydrogen bonds : bond 0.04757 / 3.53 ( 932) hydrogen bonds : angle 4.26332 / 3.05 ( 2703) link_NAG-ASN : bond 0.00335 / 0.29 ( 8) link_NAG-ASN : angle 2.65859 / 1.71 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 0.486 Fit side-chains TARDY: cannot create tardy model for: "HIS A3061 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 3274 ARG cc_start: 0.4330 (mtt180) cc_final: 0.3299 (mtp85) REVERT: A 3678 MET cc_start: 0.8550 (tpt) cc_final: 0.8169 (tpt) REVERT: A 3923 HIS cc_start: 0.6712 (t-170) cc_final: 0.5804 (t70) REVERT: A 3933 LEU cc_start: 0.6202 (mt) cc_final: 0.5944 (mm) REVERT: A 4045 ILE cc_start: 0.8428 (tt) cc_final: 0.8226 (tt) REVERT: B 251 ARG cc_start: 0.8777 (ttp-170) cc_final: 0.8575 (ttp-170) REVERT: B 456 GLN cc_start: 0.8401 (tt0) cc_final: 0.7837 (tt0) REVERT: B 643 ASP cc_start: 0.8172 (t0) cc_final: 0.7793 (t0) REVERT: C 267 LYS cc_start: 0.8450 (mmtt) cc_final: 0.7958 (pmtt) REVERT: C 373 ASP cc_start: 0.8410 (t0) cc_final: 0.8209 (t0) REVERT: C 456 GLN cc_start: 0.8510 (tt0) cc_final: 0.8041 (tt0) REVERT: C 536 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7808 (mt) REVERT: C 549 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7706 (pt0) REVERT: C 577 ILE cc_start: 0.8333 (pt) cc_final: 0.8089 (pp) REVERT: C 622 GLN cc_start: 0.8420 (mm110) cc_final: 0.8174 (mm-40) REVERT: C 643 ASP cc_start: 0.8106 (t0) cc_final: 0.7832 (t0) REVERT: C 644 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.6985 (pp) REVERT: D 234 LEU cc_start: 0.7436 (tt) cc_final: 0.7120 (tt) REVERT: D 248 TYR cc_start: 0.7206 (t80) cc_final: 0.6780 (m-80) REVERT: D 255 GLN cc_start: 0.8185 (mt0) cc_final: 0.7862 (mp10) REVERT: D 259 ASP cc_start: 0.7486 (p0) cc_final: 0.7238 (OUTLIER) REVERT: D 338 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6713 (ttp-110) REVERT: D 380 TRP cc_start: 0.6956 (t-100) cc_final: 0.6172 (m-90) REVERT: D 416 ASP cc_start: 0.8273 (m-30) cc_final: 0.7833 (m-30) REVERT: D 522 ILE cc_start: 0.7464 (mm) cc_final: 0.7201 (OUTLIER) REVERT: D 590 MET cc_start: 0.8109 (mmm) cc_final: 0.7735 (mmm) outliers start: 47 outliers final: 19 residues processed: 243 average time/residue: 0.5009 time to fit residues: 138.2320 Evaluate side-chains 219 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3286 LEU Chi-restraints excluded: chain A residue 3290 LEU Chi-restraints excluded: chain A residue 3325 VAL Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 4020 CYS Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 67 optimal weight: 4.9990 chunk 209 optimal weight: 0.3980 chunk 188 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3100 GLN A3559 HIS C 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.185656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128206 restraints weight = 20215.436| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.12 r_work: 0.3246 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17432 Z= 0.254 Angle : 0.676 9.197 23724 Z= 0.360 Chirality : 0.047 0.348 2743 Planarity : 0.005 0.076 2961 Dihedral : 5.821 54.903 2550 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.56 % Favored : 91.39 % Rotamer: Outliers : 3.69 % Allowed : 12.62 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.18), residues: 2160 helix: 1.05 (0.15), residues: 1154 sheet: -0.74 (0.38), residues: 191 loop : -2.88 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A3662 TYR 0.018 0.002 TYR C 348 PHE 0.022 0.002 PHE B 568 TRP 0.013 0.002 TRP A3922 HIS 0.008 0.001 HIS A3559 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.25 (17421) covalent geometry : angle 0.66855 / 0.36 (23694) SS BOND : bond 0.00230 / 0.11 ( 3) SS BOND : angle 2.13248 / 1.36 ( 6) hydrogen bonds : bond 0.06828 / 5.04 ( 932) hydrogen bonds : angle 4.51200 / 3.23 ( 2703) link_NAG-ASN : bond 0.00294 / 0.24 ( 8) link_NAG-ASN : angle 3.08415 / 2.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 0.660 Fit side-chains TARDY: cannot create tardy model for: "HIS A3061 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 3274 ARG cc_start: 0.4502 (mtt180) cc_final: 0.3649 (mtp85) REVERT: A 3678 MET cc_start: 0.8545 (tpt) cc_final: 0.8134 (tpt) REVERT: A 3712 ARG cc_start: 0.6890 (mmm160) cc_final: 0.6633 (mmm160) REVERT: A 3923 HIS cc_start: 0.6693 (t-170) cc_final: 0.5710 (t70) REVERT: A 3933 LEU cc_start: 0.6338 (mt) cc_final: 0.6080 (mm) REVERT: A 4087 CYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6481 (t) REVERT: B 251 ARG cc_start: 0.8857 (ttp-170) cc_final: 0.8611 (ttp-170) REVERT: B 456 GLN cc_start: 0.8456 (tt0) cc_final: 0.7875 (tt0) REVERT: B 643 ASP cc_start: 0.8305 (t0) cc_final: 0.7936 (t0) REVERT: C 267 LYS cc_start: 0.8469 (mmtt) cc_final: 0.7980 (pmtt) REVERT: C 373 ASP cc_start: 0.8493 (t0) cc_final: 0.8284 (t0) REVERT: C 456 GLN cc_start: 0.8535 (tt0) cc_final: 0.8052 (tt0) REVERT: C 494 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: C 536 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7933 (mt) REVERT: C 549 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: C 590 MET cc_start: 0.8550 (mtm) cc_final: 0.8267 (mtp) REVERT: C 622 GLN cc_start: 0.8471 (mm110) cc_final: 0.8184 (mm-40) REVERT: C 643 ASP cc_start: 0.8094 (t0) cc_final: 0.7857 (t0) REVERT: C 644 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7145 (pp) REVERT: C 675 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8041 (mtt) REVERT: D 248 TYR cc_start: 0.7252 (t80) cc_final: 0.6841 (m-80) REVERT: D 380 TRP cc_start: 0.7175 (t-100) cc_final: 0.6244 (m-90) REVERT: D 416 ASP cc_start: 0.8559 (m-30) cc_final: 0.8190 (m-30) REVERT: D 522 ILE cc_start: 0.7604 (mm) cc_final: 0.7312 (OUTLIER) outliers start: 62 outliers final: 39 residues processed: 255 average time/residue: 0.5346 time to fit residues: 155.0183 Evaluate side-chains 250 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3286 LEU Chi-restraints excluded: chain A residue 3290 LEU Chi-restraints excluded: chain A residue 3328 VAL Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3591 SER Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 4020 CYS Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4087 CYS Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 666 PHE Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 502 TYR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 71 optimal weight: 30.0000 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 6 optimal weight: 50.0000 chunk 138 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3100 GLN A3559 HIS C 543 ASN C 585 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.188933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131729 restraints weight = 20039.174| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.14 r_work: 0.3297 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17432 Z= 0.141 Angle : 0.568 8.626 23724 Z= 0.303 Chirality : 0.042 0.330 2743 Planarity : 0.004 0.043 2961 Dihedral : 5.347 53.020 2550 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.78 % Favored : 92.18 % Rotamer: Outliers : 3.27 % Allowed : 13.81 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 2160 helix: 1.34 (0.16), residues: 1150 sheet: -0.53 (0.39), residues: 186 loop : -2.77 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A3662 TYR 0.015 0.001 TYR C 348 PHE 0.019 0.001 PHE D 600 TRP 0.012 0.001 TRP A3588 HIS 0.009 0.001 HIS A3559 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (17421) covalent geometry : angle 0.56042 / 0.30 (23694) SS BOND : bond 0.00329 / 0.16 ( 3) SS BOND : angle 2.22413 / 1.41 ( 6) hydrogen bonds : bond 0.05101 / 3.78 ( 932) hydrogen bonds : angle 4.23831 / 3.03 ( 2703) link_NAG-ASN : bond 0.00313 / 0.28 ( 8) link_NAG-ASN : angle 2.85225 / 1.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 0.643 Fit side-chains TARDY: cannot create tardy model for: "HIS A3061 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 3678 MET cc_start: 0.8484 (tpt) cc_final: 0.8141 (tpt) REVERT: A 3712 ARG cc_start: 0.6972 (mmm160) cc_final: 0.6577 (mmm160) REVERT: A 3923 HIS cc_start: 0.6674 (t-170) cc_final: 0.5718 (t70) REVERT: A 3933 LEU cc_start: 0.6250 (mt) cc_final: 0.6005 (mm) REVERT: B 251 ARG cc_start: 0.8819 (ttp-170) cc_final: 0.8582 (ttp-170) REVERT: B 456 GLN cc_start: 0.8413 (tt0) cc_final: 0.7841 (tt0) REVERT: B 643 ASP cc_start: 0.8126 (t0) cc_final: 0.7731 (t0) REVERT: C 267 LYS cc_start: 0.8444 (mmtt) cc_final: 0.7976 (pmtt) REVERT: C 373 ASP cc_start: 0.8474 (t0) cc_final: 0.8213 (t0) REVERT: C 456 GLN cc_start: 0.8493 (tt0) cc_final: 0.8024 (tt0) REVERT: C 536 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7914 (mt) REVERT: C 549 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: C 577 ILE cc_start: 0.8259 (pt) cc_final: 0.8023 (pp) REVERT: C 622 GLN cc_start: 0.8470 (mm110) cc_final: 0.8211 (mm-40) REVERT: C 643 ASP cc_start: 0.8127 (t0) cc_final: 0.7827 (t0) REVERT: C 644 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7024 (pp) REVERT: D 248 TYR cc_start: 0.7237 (t80) cc_final: 0.6822 (m-80) REVERT: D 255 GLN cc_start: 0.8325 (mt0) cc_final: 0.7995 (mp10) REVERT: D 338 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.7020 (ttp-110) REVERT: D 380 TRP cc_start: 0.7059 (t-100) cc_final: 0.6290 (m-90) REVERT: D 416 ASP cc_start: 0.8274 (m-30) cc_final: 0.7852 (m-30) REVERT: D 522 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7214 (OUTLIER) outliers start: 55 outliers final: 29 residues processed: 236 average time/residue: 0.5055 time to fit residues: 136.3723 Evaluate side-chains 232 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3286 LEU Chi-restraints excluded: chain A residue 3290 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3591 SER Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 4001 LYS Chi-restraints excluded: chain A residue 4020 CYS Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 666 PHE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 502 TYR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 74 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 15 optimal weight: 50.0000 chunk 42 optimal weight: 40.0000 chunk 25 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3100 GLN A3559 HIS C 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.187256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128306 restraints weight = 20208.825| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.18 r_work: 0.3209 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17432 Z= 0.209 Angle : 0.631 8.841 23724 Z= 0.337 Chirality : 0.045 0.337 2743 Planarity : 0.004 0.062 2961 Dihedral : 5.579 53.792 2550 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.84 % Favored : 91.11 % Rotamer: Outliers : 3.33 % Allowed : 15.06 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.18), residues: 2160 helix: 1.21 (0.15), residues: 1158 sheet: -0.62 (0.39), residues: 186 loop : -2.84 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A3662 TYR 0.018 0.002 TYR C 348 PHE 0.018 0.002 PHE B 568 TRP 0.012 0.002 TRP C 414 HIS 0.013 0.001 HIS D 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (17421) covalent geometry : angle 0.62362 / 0.33 (23694) SS BOND : bond 0.00195 / 0.09 ( 3) SS BOND : angle 2.05020 / 1.24 ( 6) hydrogen bonds : bond 0.06233 / 4.61 ( 932) hydrogen bonds : angle 4.38361 / 3.13 ( 2703) link_NAG-ASN : bond 0.00273 / 0.23 ( 8) link_NAG-ASN : angle 2.98917 / 1.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 205 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 3274 ARG cc_start: 0.4476 (mtt180) cc_final: 0.3554 (mtp85) REVERT: A 3678 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8210 (tpt) REVERT: A 3712 ARG cc_start: 0.7063 (mmm160) cc_final: 0.6633 (mmm160) REVERT: A 3923 HIS cc_start: 0.6552 (t-170) cc_final: 0.5589 (t70) REVERT: A 3933 LEU cc_start: 0.6288 (mt) cc_final: 0.6042 (mm) REVERT: A 4087 CYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6465 (t) REVERT: B 251 ARG cc_start: 0.8874 (ttp-170) cc_final: 0.8638 (ttp-170) REVERT: B 294 LYS cc_start: 0.7970 (mtpp) cc_final: 0.6576 (mppt) REVERT: B 456 GLN cc_start: 0.8496 (tt0) cc_final: 0.7890 (tt0) REVERT: B 643 ASP cc_start: 0.8279 (t0) cc_final: 0.7861 (t0) REVERT: C 267 LYS cc_start: 0.8480 (mmtt) cc_final: 0.7972 (pmtt) REVERT: C 373 ASP cc_start: 0.8516 (t0) cc_final: 0.8252 (t0) REVERT: C 456 GLN cc_start: 0.8534 (tt0) cc_final: 0.8056 (tt0) REVERT: C 536 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7922 (mt) REVERT: C 549 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: C 577 ILE cc_start: 0.8307 (pt) cc_final: 0.8008 (pp) REVERT: C 622 GLN cc_start: 0.8542 (mm110) cc_final: 0.8264 (mm-40) REVERT: C 643 ASP cc_start: 0.8149 (t0) cc_final: 0.7890 (t0) REVERT: C 644 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7129 (pp) REVERT: C 698 MET cc_start: 0.4873 (OUTLIER) cc_final: 0.4619 (mtt) REVERT: D 248 TYR cc_start: 0.7209 (t80) cc_final: 0.6806 (m-80) REVERT: D 259 ASP cc_start: 0.7471 (p0) cc_final: 0.6867 (t0) REVERT: D 338 ARG cc_start: 0.7407 (ptp90) cc_final: 0.7187 (ttp-110) REVERT: D 380 TRP cc_start: 0.7075 (t-100) cc_final: 0.6230 (m-90) REVERT: D 416 ASP cc_start: 0.8469 (m-30) cc_final: 0.8099 (m-30) REVERT: D 522 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7283 (OUTLIER) outliers start: 56 outliers final: 35 residues processed: 237 average time/residue: 0.5232 time to fit residues: 141.0505 Evaluate side-chains 241 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3286 LEU Chi-restraints excluded: chain A residue 3290 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3591 SER Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 3678 MET Chi-restraints excluded: chain A residue 3897 LEU Chi-restraints excluded: chain A residue 4020 CYS Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4087 CYS Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 666 PHE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 502 TYR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 166 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 50.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3100 GLN A3559 HIS C 543 ASN C 585 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.190680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133946 restraints weight = 20113.136| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.15 r_work: 0.3326 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17432 Z= 0.114 Angle : 0.532 8.589 23724 Z= 0.285 Chirality : 0.041 0.319 2743 Planarity : 0.004 0.044 2961 Dihedral : 5.053 55.070 2550 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.50 % Favored : 92.45 % Rotamer: Outliers : 2.44 % Allowed : 16.67 % 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 are not related in a simple way. whole: -0.22 (0.19), residues: 2160 helix: 1.55 (0.16), residues: 1145 sheet: -0.47 (0.39), residues: 186 loop : -2.66 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3662 TYR 0.016 0.001 TYR C 502 PHE 0.020 0.001 PHE D 600 TRP 0.019 0.001 TRP A3298 HIS 0.010 0.001 HIS A3559 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (17421) covalent geometry : angle 0.52554 / 0.28 (23694) SS BOND : bond 0.00132 / 0.06 ( 3) SS BOND : angle 1.48682 / 1.01 ( 6) hydrogen bonds : bond 0.04433 / 3.29 ( 932) hydrogen bonds : angle 4.10262 / 2.93 ( 2703) link_NAG-ASN : bond 0.00389 / 0.33 ( 8) link_NAG-ASN : angle 2.54844 / 1.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 3678 MET cc_start: 0.8469 (tpt) cc_final: 0.8120 (tpt) REVERT: A 3712 ARG cc_start: 0.7101 (mmm160) cc_final: 0.6618 (mmm160) REVERT: A 3923 HIS cc_start: 0.6552 (t-170) cc_final: 0.5633 (t70) REVERT: A 3933 LEU cc_start: 0.6143 (mt) cc_final: 0.5886 (mm) REVERT: B 251 ARG cc_start: 0.8805 (ttp-170) cc_final: 0.8536 (ttp-170) REVERT: B 294 LYS cc_start: 0.7975 (mtpp) cc_final: 0.6561 (mppt) REVERT: B 456 GLN cc_start: 0.8461 (tt0) cc_final: 0.7879 (tt0) REVERT: B 643 ASP cc_start: 0.8037 (t0) cc_final: 0.7794 (t0) REVERT: C 267 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8026 (pmtt) REVERT: C 373 ASP cc_start: 0.8468 (t0) cc_final: 0.8230 (t0) REVERT: C 456 GLN cc_start: 0.8479 (tt0) cc_final: 0.8032 (tt0) REVERT: C 536 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7927 (mt) REVERT: C 549 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7740 (pt0) REVERT: C 590 MET cc_start: 0.8447 (mtm) cc_final: 0.8167 (mtp) REVERT: C 622 GLN cc_start: 0.8364 (mm110) cc_final: 0.8089 (mm-40) REVERT: C 643 ASP cc_start: 0.8138 (t0) cc_final: 0.7792 (t0) REVERT: C 644 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7036 (pp) REVERT: D 248 TYR cc_start: 0.7199 (t80) cc_final: 0.6809 (m-80) REVERT: D 255 GLN cc_start: 0.8263 (mt0) cc_final: 0.7884 (mp10) REVERT: D 259 ASP cc_start: 0.7548 (p0) cc_final: 0.7078 (t0) REVERT: D 380 TRP cc_start: 0.7017 (t-100) cc_final: 0.6295 (m-90) REVERT: D 416 ASP cc_start: 0.8254 (m-30) cc_final: 0.7798 (m-30) REVERT: D 522 ILE cc_start: 0.7507 (mm) cc_final: 0.7236 (OUTLIER) outliers start: 41 outliers final: 25 residues processed: 233 average time/residue: 0.4626 time to fit residues: 123.6217 Evaluate side-chains 222 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3286 LEU Chi-restraints excluded: chain A residue 3290 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3591 SER Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 666 PHE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 502 TYR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 85 optimal weight: 3.9990 chunk 21 optimal weight: 0.0270 chunk 108 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 49 optimal weight: 50.0000 chunk 6 optimal weight: 50.0000 chunk 33 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3100 GLN A3559 HIS B 580 ASN C 585 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.186144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129057 restraints weight = 20133.380| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.12 r_work: 0.3255 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17432 Z= 0.209 Angle : 0.641 8.939 23724 Z= 0.342 Chirality : 0.045 0.339 2743 Planarity : 0.004 0.060 2961 Dihedral : 5.490 53.786 2550 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.38 % Favored : 91.57 % Rotamer: Outliers : 2.80 % Allowed : 16.79 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.18), residues: 2160 helix: 1.30 (0.15), residues: 1158 sheet: -0.63 (0.39), residues: 186 loop : -2.78 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A3662 TYR 0.018 0.002 TYR C 348 PHE 0.018 0.002 PHE B 506 TRP 0.020 0.002 TRP A3298 HIS 0.011 0.001 HIS A3559 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (17421) covalent geometry : angle 0.63211 / 0.34 (23694) SS BOND : bond 0.00148 / 0.07 ( 3) SS BOND : angle 4.01284 / 2.85 ( 6) hydrogen bonds : bond 0.06136 / 4.53 ( 932) hydrogen bonds : angle 4.32327 / 3.10 ( 2703) link_NAG-ASN : bond 0.00282 / 0.23 ( 8) link_NAG-ASN : angle 2.86891 / 1.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 3274 ARG cc_start: 0.4426 (mtt180) cc_final: 0.3524 (mtp85) REVERT: A 3678 MET cc_start: 0.8494 (tpt) cc_final: 0.8211 (tpt) REVERT: A 3712 ARG cc_start: 0.7130 (mmm160) cc_final: 0.6631 (mmm160) REVERT: A 3923 HIS cc_start: 0.6489 (t-170) cc_final: 0.5581 (t70) REVERT: A 3933 LEU cc_start: 0.6194 (mt) cc_final: 0.5939 (mm) REVERT: A 3960 ASP cc_start: 0.8005 (t0) cc_final: 0.7779 (t0) REVERT: B 251 ARG cc_start: 0.8863 (ttp-170) cc_final: 0.8594 (ttp-170) REVERT: B 294 LYS cc_start: 0.8005 (mtpp) cc_final: 0.6521 (mppt) REVERT: B 456 GLN cc_start: 0.8480 (tt0) cc_final: 0.7876 (tt0) REVERT: B 643 ASP cc_start: 0.8139 (t0) cc_final: 0.7711 (t0) REVERT: C 267 LYS cc_start: 0.8471 (mmtt) cc_final: 0.7996 (pmtt) REVERT: C 373 ASP cc_start: 0.8486 (t0) cc_final: 0.8239 (t0) REVERT: C 456 GLN cc_start: 0.8490 (tt0) cc_final: 0.8021 (tt0) REVERT: C 536 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7940 (mt) REVERT: C 549 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: C 590 MET cc_start: 0.8525 (mtm) cc_final: 0.8252 (mtp) REVERT: C 622 GLN cc_start: 0.8492 (mm110) cc_final: 0.8234 (mm-40) REVERT: C 643 ASP cc_start: 0.8145 (t0) cc_final: 0.7895 (t0) REVERT: C 644 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7206 (pp) REVERT: C 698 MET cc_start: 0.4850 (OUTLIER) cc_final: 0.4594 (mtt) REVERT: D 248 TYR cc_start: 0.7234 (t80) cc_final: 0.6847 (m-80) REVERT: D 259 ASP cc_start: 0.7502 (p0) cc_final: 0.7113 (t0) REVERT: D 380 TRP cc_start: 0.7043 (t-100) cc_final: 0.6165 (m-90) REVERT: D 416 ASP cc_start: 0.8461 (m-30) cc_final: 0.8080 (m-30) REVERT: D 433 ILE cc_start: 0.4637 (OUTLIER) cc_final: 0.4320 (mp) REVERT: D 499 LYS cc_start: 0.6999 (mttt) cc_final: 0.6727 (mmtt) REVERT: D 522 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7323 (OUTLIER) outliers start: 47 outliers final: 35 residues processed: 234 average time/residue: 0.4882 time to fit residues: 130.4668 Evaluate side-chains 240 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3286 LEU Chi-restraints excluded: chain A residue 3290 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3591 SER Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 3897 LEU Chi-restraints excluded: chain A residue 4020 CYS Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 666 PHE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 502 TYR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 196 optimal weight: 0.0050 chunk 92 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 8 optimal weight: 50.0000 chunk 123 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3100 GLN A3559 HIS C 543 ASN C 585 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.190758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134248 restraints weight = 20039.963| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.15 r_work: 0.3325 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17432 Z= 0.116 Angle : 0.552 9.116 23724 Z= 0.294 Chirality : 0.041 0.319 2743 Planarity : 0.004 0.043 2961 Dihedral : 5.005 56.691 2550 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.64 % Favored : 92.31 % Rotamer: Outliers : 2.14 % Allowed : 17.68 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 2160 helix: 1.58 (0.16), residues: 1154 sheet: -0.48 (0.39), residues: 186 loop : -2.64 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3662 TYR 0.016 0.001 TYR C 502 PHE 0.029 0.001 PHE B 506 TRP 0.019 0.001 TRP A3298 HIS 0.011 0.001 HIS A3559 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (17421) covalent geometry : angle 0.54353 / 0.29 (23694) SS BOND : bond 0.00174 / 0.08 ( 3) SS BOND : angle 3.38119 / 2.80 ( 6) hydrogen bonds : bond 0.04351 / 3.23 ( 932) hydrogen bonds : angle 4.07190 / 2.91 ( 2703) link_NAG-ASN : bond 0.00375 / 0.32 ( 8) link_NAG-ASN : angle 2.47853 / 1.62 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 3678 MET cc_start: 0.8456 (tpt) cc_final: 0.8099 (tpt) REVERT: A 3712 ARG cc_start: 0.7129 (mmm160) cc_final: 0.6622 (mmm160) REVERT: A 3923 HIS cc_start: 0.6436 (t-170) cc_final: 0.5643 (t70) REVERT: A 3933 LEU cc_start: 0.6072 (mt) cc_final: 0.5801 (mm) REVERT: B 251 ARG cc_start: 0.8799 (ttp-170) cc_final: 0.8525 (ttp-170) REVERT: B 294 LYS cc_start: 0.7997 (mtpp) cc_final: 0.6476 (mppt) REVERT: B 456 GLN cc_start: 0.8428 (tt0) cc_final: 0.7831 (tt0) REVERT: B 583 MET cc_start: 0.8606 (mmm) cc_final: 0.8300 (mmp) REVERT: B 643 ASP cc_start: 0.7984 (t0) cc_final: 0.7556 (t0) REVERT: C 267 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8028 (pmtt) REVERT: C 373 ASP cc_start: 0.8462 (t0) cc_final: 0.8222 (t0) REVERT: C 456 GLN cc_start: 0.8453 (tt0) cc_final: 0.8012 (tt0) REVERT: C 536 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7933 (mt) REVERT: C 549 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7717 (pt0) REVERT: C 590 MET cc_start: 0.8376 (mtm) cc_final: 0.8119 (mtp) REVERT: C 622 GLN cc_start: 0.8337 (mm110) cc_final: 0.8083 (mm-40) REVERT: C 643 ASP cc_start: 0.8115 (t0) cc_final: 0.7808 (t0) REVERT: C 644 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7049 (pp) REVERT: C 698 MET cc_start: 0.4757 (mtm) cc_final: 0.4495 (mtt) REVERT: D 248 TYR cc_start: 0.7210 (t80) cc_final: 0.6835 (m-80) REVERT: D 255 GLN cc_start: 0.8310 (mt0) cc_final: 0.7924 (mp10) REVERT: D 259 ASP cc_start: 0.7555 (p0) cc_final: 0.7172 (t0) REVERT: D 380 TRP cc_start: 0.7069 (t-100) cc_final: 0.6327 (m-90) REVERT: D 416 ASP cc_start: 0.8254 (m-30) cc_final: 0.7792 (m-30) REVERT: D 433 ILE cc_start: 0.4483 (OUTLIER) cc_final: 0.4135 (mp) outliers start: 36 outliers final: 28 residues processed: 232 average time/residue: 0.4507 time to fit residues: 120.3841 Evaluate side-chains 236 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3286 LEU Chi-restraints excluded: chain A residue 3290 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3337 TYR Chi-restraints excluded: chain A residue 3591 SER Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 666 PHE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 502 TYR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 59 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 171 optimal weight: 0.0970 chunk 108 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3100 GLN A3559 HIS A3695 HIS B 434 ASN C 525 ASN C 585 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.191939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.139003 restraints weight = 19959.421| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.40 r_work: 0.3340 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17432 Z= 0.111 Angle : 0.536 10.567 23724 Z= 0.287 Chirality : 0.040 0.304 2743 Planarity : 0.004 0.043 2961 Dihedral : 4.795 59.225 2550 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.82 % Favored : 92.13 % Rotamer: Outliers : 1.85 % Allowed : 18.04 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.19), residues: 2160 helix: 1.72 (0.16), residues: 1154 sheet: -0.40 (0.39), residues: 186 loop : -2.56 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3662 TYR 0.020 0.001 TYR D 486 PHE 0.025 0.001 PHE C 485 TRP 0.022 0.001 TRP A3298 HIS 0.012 0.001 HIS A3559 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (17421) covalent geometry : angle 0.52921 / 0.29 (23694) SS BOND : bond 0.00069 / 0.03 ( 3) SS BOND : angle 3.11768 / 2.54 ( 6) hydrogen bonds : bond 0.04120 / 3.06 ( 932) hydrogen bonds : angle 3.98432 / 2.85 ( 2703) link_NAG-ASN : bond 0.00355 / 0.30 ( 8) link_NAG-ASN : angle 2.28977 / 1.51 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 3274 ARG cc_start: 0.4167 (mtt180) cc_final: 0.3404 (mtp85) REVERT: A 3678 MET cc_start: 0.8485 (tpt) cc_final: 0.8107 (tpt) REVERT: A 3723 LEU cc_start: 0.7034 (pp) cc_final: 0.6402 (mp) REVERT: A 3923 HIS cc_start: 0.6732 (t-170) cc_final: 0.5903 (t70) REVERT: A 3933 LEU cc_start: 0.6215 (mt) cc_final: 0.5946 (mm) REVERT: B 294 LYS cc_start: 0.8034 (mtpp) cc_final: 0.6524 (mppt) REVERT: B 456 GLN cc_start: 0.8462 (tt0) cc_final: 0.7905 (tm-30) REVERT: B 583 MET cc_start: 0.8635 (mmm) cc_final: 0.8240 (mmp) REVERT: B 643 ASP cc_start: 0.8011 (t0) cc_final: 0.7755 (t0) REVERT: C 241 MET cc_start: 0.7128 (ttm) cc_final: 0.6879 (ttt) REVERT: C 267 LYS cc_start: 0.8469 (mmtt) cc_final: 0.7995 (pmtt) REVERT: C 353 GLU cc_start: 0.9021 (pt0) cc_final: 0.8716 (pt0) REVERT: C 456 GLN cc_start: 0.8525 (tt0) cc_final: 0.8105 (tp40) REVERT: C 536 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8018 (mt) REVERT: C 549 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: C 590 MET cc_start: 0.8503 (mtm) cc_final: 0.8266 (mtp) REVERT: C 622 GLN cc_start: 0.8329 (mm110) cc_final: 0.8066 (mm-40) REVERT: C 643 ASP cc_start: 0.8052 (t0) cc_final: 0.7758 (t0) REVERT: C 644 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7172 (pp) REVERT: C 698 MET cc_start: 0.4701 (mtm) cc_final: 0.4439 (mtt) REVERT: D 248 TYR cc_start: 0.7264 (t80) cc_final: 0.6902 (m-80) REVERT: D 255 GLN cc_start: 0.8477 (mt0) cc_final: 0.8127 (mp10) REVERT: D 259 ASP cc_start: 0.7539 (p0) cc_final: 0.7201 (t0) REVERT: D 380 TRP cc_start: 0.7078 (t-100) cc_final: 0.6340 (m-90) REVERT: D 416 ASP cc_start: 0.8314 (m-30) cc_final: 0.7867 (m-30) REVERT: D 433 ILE cc_start: 0.4503 (OUTLIER) cc_final: 0.4165 (mp) outliers start: 31 outliers final: 23 residues processed: 226 average time/residue: 0.4533 time to fit residues: 117.8127 Evaluate side-chains 223 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3286 LEU Chi-restraints excluded: chain A residue 3290 LEU Chi-restraints excluded: chain A residue 3591 SER Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 666 PHE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 502 TYR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 193 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 chunk 170 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 49 optimal weight: 30.0000 chunk 162 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 45 optimal weight: 40.0000 chunk 166 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3100 GLN A3559 HIS C 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.187416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128809 restraints weight = 20180.121| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.18 r_work: 0.3257 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17432 Z= 0.206 Angle : 0.644 10.122 23724 Z= 0.344 Chirality : 0.045 0.339 2743 Planarity : 0.004 0.062 2961 Dihedral : 5.379 55.476 2550 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.56 % Favored : 91.39 % Rotamer: Outliers : 2.32 % Allowed : 17.92 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.19), residues: 2160 helix: 1.44 (0.15), residues: 1156 sheet: -0.56 (0.38), residues: 186 loop : -2.70 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 528 TYR 0.018 0.002 TYR C 348 PHE 0.018 0.002 PHE D 600 TRP 0.026 0.002 TRP A3298 HIS 0.011 0.001 HIS A3559 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (17421) covalent geometry : angle 0.63594 / 0.34 (23694) SS BOND : bond 0.00228 / 0.11 ( 3) SS BOND : angle 3.82876 / 2.90 ( 6) hydrogen bonds : bond 0.06007 / 4.44 ( 932) hydrogen bonds : angle 4.27416 / 3.07 ( 2703) link_NAG-ASN : bond 0.00291 / 0.24 ( 8) link_NAG-ASN : angle 2.74444 / 1.82 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6745.65 seconds wall clock time: 115 minutes 15.13 seconds (6915.13 seconds total)