Starting phenix.real_space_refine on Thu Jul 2 18:12:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dti_27699/07_2026/8dti_27699.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dti_27699/07_2026/8dti_27699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dti_27699/07_2026/8dti_27699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dti_27699/07_2026/8dti_27699.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dti_27699/07_2026/8dti_27699.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dti_27699/07_2026/8dti_27699.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dti_27699/07_2026/8dti_27699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dti_27699/07_2026/8dti_27699.map" } resolution = 3.8 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= 0.002 sd= 0.976 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 63 5.16 5 C 6018 2.51 5 N 1594 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 9455 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4684 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 598} Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 14, 'ASN:plan1': 1, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 134 Chain: "B" Number of atoms: 4695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4695 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 598} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 13, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 125 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GFB': 1} Classifications: {'RNA_mixed': 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GFB': 1} Classifications: {'RNA_mixed': 1} Time building chain proxies: 1.77, per 1000 atoms: 0.19 Number of scatterers: 9455 At special positions: 0 Unit cell: (156.6, 78.84, 78.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 4 15.00 O 1776 8.00 N 1594 7.00 C 6018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 296.0 milliseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 4 sheets defined 66.0% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.707A pdb=" N TYR A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 250 Processing helix chain 'A' and resid 253 through 275 Processing helix chain 'A' and resid 276 through 291 Processing helix chain 'A' and resid 294 through 308 removed outlier: 3.620A pdb=" N MET A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 325 Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 378 through 393 Processing helix chain 'A' and resid 396 through 411 removed outlier: 4.051A pdb=" N PHE A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 450 through 467 Processing helix chain 'A' and resid 495 through 508 removed outlier: 4.323A pdb=" N ALA A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 525 through 539 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 576 through 581 removed outlier: 3.955A pdb=" N MET A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 667 through 681 removed outlier: 3.574A pdb=" N VAL A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 732 through 735 Processing helix chain 'A' and resid 747 through 756 removed outlier: 3.638A pdb=" N CYS A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 removed outlier: 4.728A pdb=" N GLY A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL A 774 " --> pdb=" O HIS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 789 through 803 removed outlier: 4.208A pdb=" N ASP A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 820 removed outlier: 4.203A pdb=" N ARG A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP A 816 " --> pdb=" O MET A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 846 removed outlier: 3.955A pdb=" N PHE A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 234 removed outlier: 3.709A pdb=" N TYR B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 250 Processing helix chain 'B' and resid 253 through 275 Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.621A pdb=" N MET B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 325 Processing helix chain 'B' and resid 328 through 342 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 378 through 393 Processing helix chain 'B' and resid 396 through 411 removed outlier: 4.050A pdb=" N PHE B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 430 through 442 Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 450 through 467 Processing helix chain 'B' and resid 495 through 508 removed outlier: 4.323A pdb=" N ALA B 503 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Proline residue: B 504 - end of helix Processing helix chain 'B' and resid 525 through 539 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 576 through 581 removed outlier: 3.956A pdb=" N MET B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 653 Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'B' and resid 667 through 681 removed outlier: 3.575A pdb=" N VAL B 681 " --> pdb=" O ILE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 709 Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 732 through 735 Processing helix chain 'B' and resid 747 through 756 removed outlier: 3.638A pdb=" N CYS B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 781 removed outlier: 4.729A pdb=" N GLY B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL B 774 " --> pdb=" O HIS B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 789 through 803 removed outlier: 4.208A pdb=" N ASP B 803 " --> pdb=" O ASP B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 820 removed outlier: 4.203A pdb=" N ARG B 815 " --> pdb=" O ARG B 811 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP B 816 " --> pdb=" O MET B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 846 removed outlier: 3.954A pdb=" N PHE B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 541 through 544 removed outlier: 6.212A pdb=" N THR A 484 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 566 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY A 486 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN A 588 " --> pdb=" O TYR A 605 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE A 607 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR A 590 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N ASP A 609 " --> pdb=" O THR A 590 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 606 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU A 628 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 608 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 716 through 719 removed outlier: 8.840A pdb=" N ASP A 717 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A 686 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU A 719 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 688 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 655 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 687 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE A 657 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N LYS A 689 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER A 659 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 737 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER A 738 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N MET A 763 " --> pdb=" O SER A 738 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ALA A 787 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A 762 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 541 through 544 removed outlier: 6.212A pdb=" N THR B 484 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL B 566 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY B 486 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN B 588 " --> pdb=" O TYR B 605 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE B 607 " --> pdb=" O GLN B 588 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR B 590 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N ASP B 609 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG B 606 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU B 628 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR B 608 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 716 through 719 removed outlier: 8.840A pdb=" N ASP B 717 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU B 686 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU B 719 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 688 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 655 " --> pdb=" O ARG B 685 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL B 687 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE B 657 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LYS B 689 " --> pdb=" O PHE B 657 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER B 659 " --> pdb=" O LYS B 689 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 737 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER B 738 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N MET B 763 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ALA B 787 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR B 762 " --> pdb=" O ALA B 787 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1952 1.33 - 1.45: 2285 1.45 - 1.57: 5347 1.57 - 1.69: 8 1.69 - 1.81: 95 Bond restraints: 9687 Sorted by residual: bond pdb=" C4 GFB A1001 " pdb=" N3 GFB A1001 " ideal model delta sigma weight residual 1.340 1.503 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" C4 GFB B1001 " pdb=" N3 GFB B1001 " ideal model delta sigma weight residual 1.340 1.503 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" C2 GFB A1001 " pdb=" N2 GFB A1001 " ideal model delta sigma weight residual 1.341 1.491 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C2 GFB B1001 " pdb=" N2 GFB B1001 " ideal model delta sigma weight residual 1.341 1.490 -0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" C2 GFB B1001 " pdb=" N3 GFB B1001 " ideal model delta sigma weight residual 1.310 1.451 -0.141 2.00e-02 2.50e+03 4.98e+01 ... (remaining 9682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 13161 3.10 - 6.21: 83 6.21 - 9.31: 10 9.31 - 12.41: 4 12.41 - 15.51: 4 Bond angle restraints: 13262 Sorted by residual: angle pdb=" O2P GFB B1001 " pdb=" P GFB B1001 " pdb=" O5' GFB B1001 " ideal model delta sigma weight residual 93.35 108.86 -15.51 3.00e+00 1.11e-01 2.67e+01 angle pdb=" O2P GFB A1001 " pdb=" P GFB A1001 " pdb=" O5' GFB A1001 " ideal model delta sigma weight residual 93.35 108.84 -15.49 3.00e+00 1.11e-01 2.66e+01 angle pdb=" O1X GFB A1001 " pdb=" P1 GFB A1001 " pdb=" O2X GFB A1001 " ideal model delta sigma weight residual 122.73 109.50 13.23 3.00e+00 1.11e-01 1.94e+01 angle pdb=" O1X GFB B1001 " pdb=" P1 GFB B1001 " pdb=" O2X GFB B1001 " ideal model delta sigma weight residual 122.73 109.55 13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" O1 GFB A1001 " pdb=" P1 GFB A1001 " pdb=" O2P GFB A1001 " ideal model delta sigma weight residual 99.26 109.54 -10.28 3.00e+00 1.11e-01 1.17e+01 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 5076 15.94 - 31.88: 450 31.88 - 47.82: 126 47.82 - 63.76: 18 63.76 - 79.70: 6 Dihedral angle restraints: 5676 sinusoidal: 1982 harmonic: 3694 Sorted by residual: dihedral pdb=" CG ARG A 532 " pdb=" CD ARG A 532 " pdb=" NE ARG A 532 " pdb=" CZ ARG A 532 " ideal model delta sinusoidal sigma weight residual -180.00 -137.41 -42.59 2 1.50e+01 4.44e-03 9.77e+00 dihedral pdb=" CG ARG B 532 " pdb=" CD ARG B 532 " pdb=" NE ARG B 532 " pdb=" CZ ARG B 532 " ideal model delta sinusoidal sigma weight residual -180.00 -137.46 -42.54 2 1.50e+01 4.44e-03 9.75e+00 dihedral pdb=" CB MET B 441 " pdb=" CG MET B 441 " pdb=" SD MET B 441 " pdb=" CE MET B 441 " ideal model delta sinusoidal sigma weight residual -180.00 -120.28 -59.72 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1368 0.070 - 0.140: 149 0.140 - 0.209: 4 0.209 - 0.279: 0 0.279 - 0.349: 2 Chirality restraints: 1523 Sorted by residual: chirality pdb=" C2' GFB B1001 " pdb=" C1' GFB B1001 " pdb=" C3' GFB B1001 " pdb=" O2' GFB B1001 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C2' GFB A1001 " pdb=" C1' GFB A1001 " pdb=" C3' GFB A1001 " pdb=" O2' GFB A1001 " both_signs ideal model delta sigma weight residual False -2.56 -2.90 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C5A GFB B1001 " pdb=" C4A GFB B1001 " pdb=" C6A GFB B1001 " pdb=" O5 GFB B1001 " both_signs ideal model delta sigma weight residual False 2.42 2.63 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1520 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 420 " 0.022 2.00e-02 2.50e+03 1.87e-02 7.02e+00 pdb=" CG TYR B 420 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 420 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 420 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 420 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 420 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 420 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 420 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 420 " -0.022 2.00e-02 2.50e+03 1.87e-02 6.97e+00 pdb=" CG TYR A 420 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 420 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 420 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 420 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 420 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 420 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 420 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 420 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C TYR B 420 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR B 420 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU B 421 " 0.008 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 731 2.74 - 3.28: 10009 3.28 - 3.82: 16216 3.82 - 4.36: 17902 4.36 - 4.90: 30474 Nonbonded interactions: 75332 Sorted by model distance: nonbonded pdb=" OG1 THR A 748 " pdb=" OE2 GLU A 752 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR B 748 " pdb=" OE2 GLU B 752 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR B 518 " pdb=" OD2 ASP B 560 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR A 518 " pdb=" OD2 ASP A 560 " model vdw 2.214 3.040 nonbonded pdb=" O LEU A 505 " pdb=" OH TYR A 510 " model vdw 2.231 3.040 ... (remaining 75327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 218 through 226 and (name N or name CA or name C or name \ O or name CB )) or resid 227 or (resid 228 through 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 1001)) selection = (chain 'B' and (resid 218 through 232 or (resid 233 and (name N or name CA or na \ me C or name O or name CB )) or resid 234 through 236 or (resid 237 through 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 77 \ 8 or (resid 779 and (name N or name CA or name C or name O or name CB )) or resi \ d 780 through 1001)) } 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 group one per residue 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.163 9687 Z= 0.314 Angle : 0.659 15.513 13262 Z= 0.306 Chirality : 0.041 0.349 1523 Planarity : 0.003 0.032 1702 Dihedral : 13.313 79.702 3304 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.25), residues: 1254 helix: 2.19 (0.19), residues: 778 sheet: 0.11 (0.49), residues: 122 loop : -0.63 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.045 0.001 TYR B 420 PHE 0.018 0.001 PHE A 724 TRP 0.007 0.001 TRP B 459 HIS 0.003 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.31 ( 9687) covalent geometry : angle 0.65877 / 0.31 (13262) hydrogen bonds : bond 0.14633 / 10.48 ( 582) hydrogen bonds : angle 5.03662 / 3.74 ( 1722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.269 Fit side-chains REVERT: A 632 PHE cc_start: 0.6534 (p90) cc_final: 0.6318 (p90) REVERT: B 632 PHE cc_start: 0.7292 (p90) cc_final: 0.7026 (p90) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0544 time to fit residues: 10.7711 Evaluate side-chains 98 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 ASN A 467 HIS B 368 ASN ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.117594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099833 restraints weight = 21333.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102676 restraints weight = 13098.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104656 restraints weight = 9233.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106081 restraints weight = 7099.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.106979 restraints weight = 5814.086| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9687 Z= 0.156 Angle : 0.527 7.588 13262 Z= 0.267 Chirality : 0.041 0.146 1523 Planarity : 0.004 0.027 1702 Dihedral : 4.133 40.323 1365 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.96 % Allowed : 8.25 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 1254 helix: 2.42 (0.19), residues: 792 sheet: -0.53 (0.46), residues: 130 loop : -0.55 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.025 0.002 TYR B 420 PHE 0.023 0.002 PHE B 500 TRP 0.012 0.001 TRP B 473 HIS 0.008 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 9687) covalent geometry : angle 0.52686 / 0.27 (13262) hydrogen bonds : bond 0.03935 / 2.77 ( 582) hydrogen bonds : angle 4.02242 / 3.01 ( 1722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.349 Fit side-chains REVERT: A 318 TYR cc_start: 0.8586 (m-80) cc_final: 0.7850 (m-80) REVERT: A 632 PHE cc_start: 0.6874 (p90) cc_final: 0.6612 (p90) REVERT: A 729 MET cc_start: 0.8003 (tpp) cc_final: 0.7793 (tpp) REVERT: B 290 TYR cc_start: 0.8659 (m-80) cc_final: 0.8436 (m-80) REVERT: B 508 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7146 (t-90) REVERT: B 632 PHE cc_start: 0.7674 (p90) cc_final: 0.7094 (p90) outliers start: 9 outliers final: 6 residues processed: 117 average time/residue: 0.0552 time to fit residues: 10.5692 Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 723 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 56 optimal weight: 0.0040 chunk 25 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.094972 restraints weight = 21652.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097732 restraints weight = 13466.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099704 restraints weight = 9616.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101093 restraints weight = 7470.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.102081 restraints weight = 6164.717| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9687 Z= 0.220 Angle : 0.579 6.037 13262 Z= 0.297 Chirality : 0.042 0.134 1523 Planarity : 0.004 0.037 1702 Dihedral : 4.408 42.230 1365 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 12.65 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1254 helix: 2.15 (0.18), residues: 802 sheet: -0.90 (0.51), residues: 110 loop : -0.53 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 606 TYR 0.024 0.002 TYR B 318 PHE 0.040 0.002 PHE A 724 TRP 0.010 0.001 TRP A 459 HIS 0.006 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 ( 9687) covalent geometry : angle 0.57913 / 0.30 (13262) hydrogen bonds : bond 0.04220 / 2.94 ( 582) hydrogen bonds : angle 4.14755 / 3.10 ( 1722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.229 Fit side-chains REVERT: A 318 TYR cc_start: 0.8479 (m-80) cc_final: 0.7783 (m-80) REVERT: A 491 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7534 (p0) REVERT: A 632 PHE cc_start: 0.6819 (p90) cc_final: 0.6510 (p90) REVERT: B 290 TYR cc_start: 0.8707 (m-80) cc_final: 0.8503 (m-80) REVERT: B 508 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7099 (t-90) REVERT: B 632 PHE cc_start: 0.7526 (p90) cc_final: 0.6894 (p90) outliers start: 18 outliers final: 13 residues processed: 113 average time/residue: 0.0542 time to fit residues: 10.2291 Evaluate side-chains 110 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 chunk 107 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN B 661 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.115892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097881 restraints weight = 21474.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100799 restraints weight = 13252.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102832 restraints weight = 9333.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104286 restraints weight = 7177.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105313 restraints weight = 5851.823| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9687 Z= 0.107 Angle : 0.499 6.341 13262 Z= 0.250 Chirality : 0.040 0.125 1523 Planarity : 0.003 0.033 1702 Dihedral : 4.204 39.629 1365 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.14 % Allowed : 13.83 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.25), residues: 1254 helix: 2.58 (0.18), residues: 778 sheet: -0.79 (0.45), residues: 140 loop : -0.57 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.015 0.001 TYR B 420 PHE 0.015 0.002 PHE B 724 TRP 0.006 0.001 TRP B 459 HIS 0.003 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9687) covalent geometry : angle 0.49944 / 0.25 (13262) hydrogen bonds : bond 0.03193 / 2.24 ( 582) hydrogen bonds : angle 3.71092 / 2.77 ( 1722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.310 Fit side-chains REVERT: A 318 TYR cc_start: 0.8429 (m-80) cc_final: 0.7804 (m-80) REVERT: A 594 TYR cc_start: 0.8191 (t80) cc_final: 0.7980 (t80) REVERT: A 632 PHE cc_start: 0.6604 (p90) cc_final: 0.6320 (p90) REVERT: B 491 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7138 (p0) REVERT: B 508 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.7136 (t-90) REVERT: B 632 PHE cc_start: 0.7577 (p90) cc_final: 0.6875 (p90) outliers start: 20 outliers final: 14 residues processed: 118 average time/residue: 0.0517 time to fit residues: 9.7573 Evaluate side-chains 113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.113541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.095193 restraints weight = 21688.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.098096 restraints weight = 13528.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100084 restraints weight = 9606.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.101507 restraints weight = 7471.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.102471 restraints weight = 6159.265| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9687 Z= 0.163 Angle : 0.535 7.073 13262 Z= 0.270 Chirality : 0.041 0.123 1523 Planarity : 0.004 0.035 1702 Dihedral : 4.273 40.081 1365 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.00 % Allowed : 14.26 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.24), residues: 1254 helix: 2.52 (0.18), residues: 780 sheet: -0.23 (0.49), residues: 118 loop : -0.84 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 233 TYR 0.018 0.001 TYR B 793 PHE 0.020 0.002 PHE A 724 TRP 0.008 0.001 TRP A 459 HIS 0.005 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9687) covalent geometry : angle 0.53482 / 0.27 (13262) hydrogen bonds : bond 0.03648 / 2.54 ( 582) hydrogen bonds : angle 3.73577 / 2.80 ( 1722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.397 Fit side-chains REVERT: A 318 TYR cc_start: 0.8404 (m-80) cc_final: 0.7759 (m-80) REVERT: A 491 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7289 (p0) REVERT: A 814 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8492 (tt) REVERT: B 491 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7432 (p0) REVERT: B 508 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7116 (t-90) REVERT: B 632 PHE cc_start: 0.7564 (p90) cc_final: 0.6877 (p90) outliers start: 28 outliers final: 16 residues processed: 117 average time/residue: 0.0609 time to fit residues: 11.6737 Evaluate side-chains 115 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 0.0020 chunk 111 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.114978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096863 restraints weight = 21561.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099798 restraints weight = 13386.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101812 restraints weight = 9465.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103224 restraints weight = 7332.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104193 restraints weight = 6020.440| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9687 Z= 0.114 Angle : 0.501 6.520 13262 Z= 0.252 Chirality : 0.039 0.121 1523 Planarity : 0.004 0.034 1702 Dihedral : 4.181 38.551 1365 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.11 % Allowed : 15.22 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.25), residues: 1254 helix: 2.57 (0.18), residues: 790 sheet: -0.23 (0.46), residues: 130 loop : -1.05 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 606 TYR 0.016 0.001 TYR B 546 PHE 0.022 0.001 PHE A 724 TRP 0.006 0.001 TRP A 459 HIS 0.003 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9687) covalent geometry : angle 0.50120 / 0.25 (13262) hydrogen bonds : bond 0.03117 / 2.17 ( 582) hydrogen bonds : angle 3.49443 / 2.62 ( 1722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.375 Fit side-chains REVERT: A 232 ASN cc_start: 0.5960 (p0) cc_final: 0.5701 (p0) REVERT: A 318 TYR cc_start: 0.8406 (m-80) cc_final: 0.7760 (m-80) REVERT: A 814 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8541 (tt) REVERT: B 491 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7330 (p0) REVERT: B 508 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7168 (t-90) REVERT: B 632 PHE cc_start: 0.7553 (p90) cc_final: 0.6853 (p90) outliers start: 29 outliers final: 20 residues processed: 122 average time/residue: 0.0671 time to fit residues: 13.2152 Evaluate side-chains 119 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.115057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096850 restraints weight = 21556.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099741 restraints weight = 13418.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.101775 restraints weight = 9534.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.103208 restraints weight = 7377.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104110 restraints weight = 6052.103| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9687 Z= 0.115 Angle : 0.511 6.592 13262 Z= 0.254 Chirality : 0.039 0.120 1523 Planarity : 0.003 0.033 1702 Dihedral : 4.128 37.726 1365 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.68 % Allowed : 15.76 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.24), residues: 1254 helix: 2.59 (0.18), residues: 790 sheet: -0.24 (0.46), residues: 130 loop : -1.04 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 715 TYR 0.018 0.001 TYR A 594 PHE 0.023 0.001 PHE A 724 TRP 0.006 0.001 TRP A 459 HIS 0.003 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 9687) covalent geometry : angle 0.51115 / 0.25 (13262) hydrogen bonds : bond 0.03124 / 2.18 ( 582) hydrogen bonds : angle 3.43921 / 2.58 ( 1722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.366 Fit side-chains REVERT: A 232 ASN cc_start: 0.5888 (p0) cc_final: 0.5446 (p0) REVERT: A 318 TYR cc_start: 0.8398 (m-80) cc_final: 0.7756 (m-80) REVERT: A 491 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7124 (p0) REVERT: A 814 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8550 (tt) REVERT: B 491 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7300 (p0) REVERT: B 508 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.7196 (t-90) REVERT: B 632 PHE cc_start: 0.7570 (p90) cc_final: 0.6843 (p90) outliers start: 25 outliers final: 19 residues processed: 117 average time/residue: 0.0606 time to fit residues: 11.6479 Evaluate side-chains 118 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.114594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096191 restraints weight = 21579.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.099093 restraints weight = 13472.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.101124 restraints weight = 9629.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102561 restraints weight = 7481.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103474 restraints weight = 6162.751| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9687 Z= 0.129 Angle : 0.523 6.819 13262 Z= 0.262 Chirality : 0.040 0.137 1523 Planarity : 0.004 0.033 1702 Dihedral : 4.157 37.857 1365 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.43 % Allowed : 15.65 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.24), residues: 1254 helix: 2.56 (0.18), residues: 790 sheet: -0.29 (0.46), residues: 130 loop : -1.07 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 685 TYR 0.020 0.001 TYR B 318 PHE 0.024 0.001 PHE A 724 TRP 0.006 0.001 TRP A 459 HIS 0.004 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9687) covalent geometry : angle 0.52297 / 0.26 (13262) hydrogen bonds : bond 0.03245 / 2.26 ( 582) hydrogen bonds : angle 3.52901 / 2.65 ( 1722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.365 Fit side-chains REVERT: A 232 ASN cc_start: 0.5958 (p0) cc_final: 0.5484 (p0) REVERT: A 318 TYR cc_start: 0.8382 (m-80) cc_final: 0.7768 (m-80) REVERT: A 491 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7142 (p0) REVERT: A 777 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7194 (mm) REVERT: A 814 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8558 (tt) REVERT: B 491 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7393 (p0) REVERT: B 508 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.7210 (t-90) REVERT: B 632 PHE cc_start: 0.7551 (p90) cc_final: 0.6790 (p90) outliers start: 32 outliers final: 23 residues processed: 123 average time/residue: 0.0596 time to fit residues: 12.0448 Evaluate side-chains 125 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 60 optimal weight: 0.0570 chunk 29 optimal weight: 0.9990 chunk 92 optimal weight: 0.0000 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.116405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.098117 restraints weight = 21425.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.101099 restraints weight = 13335.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.103165 restraints weight = 9449.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.104637 restraints weight = 7291.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.105645 restraints weight = 5968.025| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9687 Z= 0.098 Angle : 0.515 7.851 13262 Z= 0.254 Chirality : 0.039 0.127 1523 Planarity : 0.003 0.032 1702 Dihedral : 4.078 36.283 1365 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.68 % Allowed : 16.51 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.25), residues: 1254 helix: 2.64 (0.18), residues: 790 sheet: -0.23 (0.46), residues: 130 loop : -0.98 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 606 TYR 0.021 0.001 TYR A 299 PHE 0.025 0.001 PHE A 724 TRP 0.005 0.001 TRP B 461 HIS 0.002 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 9687) covalent geometry : angle 0.51504 / 0.25 (13262) hydrogen bonds : bond 0.02972 / 2.08 ( 582) hydrogen bonds : angle 3.36989 / 2.54 ( 1722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.299 Fit side-chains REVERT: A 232 ASN cc_start: 0.5948 (p0) cc_final: 0.5532 (p0) REVERT: A 318 TYR cc_start: 0.8364 (m-80) cc_final: 0.7771 (m-80) REVERT: A 491 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.6833 (p0) REVERT: A 777 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7310 (mm) REVERT: A 814 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8522 (tt) REVERT: B 491 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7109 (p0) REVERT: B 632 PHE cc_start: 0.7542 (p90) cc_final: 0.6768 (p90) outliers start: 25 outliers final: 18 residues processed: 124 average time/residue: 0.0670 time to fit residues: 13.4293 Evaluate side-chains 118 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 98 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.114953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096666 restraints weight = 21502.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099531 restraints weight = 13450.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.101542 restraints weight = 9574.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.102991 restraints weight = 7426.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104043 restraints weight = 6100.359| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9687 Z= 0.121 Angle : 0.528 7.134 13262 Z= 0.261 Chirality : 0.040 0.130 1523 Planarity : 0.003 0.032 1702 Dihedral : 4.084 36.994 1365 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.57 % Allowed : 16.72 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.25), residues: 1254 helix: 2.54 (0.18), residues: 802 sheet: -0.36 (0.50), residues: 110 loop : -0.95 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 715 TYR 0.015 0.001 TYR A 546 PHE 0.025 0.001 PHE A 724 TRP 0.007 0.001 TRP B 461 HIS 0.003 0.001 HIS A 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9687) covalent geometry : angle 0.52810 / 0.26 (13262) hydrogen bonds : bond 0.03180 / 2.21 ( 582) hydrogen bonds : angle 3.41809 / 2.56 ( 1722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.371 Fit side-chains REVERT: A 232 ASN cc_start: 0.5865 (p0) cc_final: 0.5364 (p0) REVERT: A 318 TYR cc_start: 0.8344 (m-80) cc_final: 0.7729 (m-80) REVERT: A 491 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.6927 (p0) REVERT: A 814 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8543 (tt) REVERT: B 491 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7127 (p0) REVERT: B 632 PHE cc_start: 0.7474 (p90) cc_final: 0.6747 (p90) outliers start: 24 outliers final: 20 residues processed: 120 average time/residue: 0.0661 time to fit residues: 12.9529 Evaluate side-chains 121 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.115679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097573 restraints weight = 21313.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100502 restraints weight = 13279.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102521 restraints weight = 9390.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103865 restraints weight = 7260.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104968 restraints weight = 6003.832| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9687 Z= 0.106 Angle : 0.524 8.552 13262 Z= 0.257 Chirality : 0.039 0.131 1523 Planarity : 0.003 0.032 1702 Dihedral : 4.049 36.378 1365 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.79 % Allowed : 16.83 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.24), residues: 1254 helix: 2.53 (0.18), residues: 802 sheet: -0.31 (0.50), residues: 110 loop : -0.94 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 811 TYR 0.033 0.001 TYR B 318 PHE 0.026 0.001 PHE A 724 TRP 0.006 0.001 TRP B 461 HIS 0.002 0.001 HIS B 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 9687) covalent geometry : angle 0.52405 / 0.26 (13262) hydrogen bonds : bond 0.03024 / 2.11 ( 582) hydrogen bonds : angle 3.36039 / 2.52 ( 1722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1382.90 seconds wall clock time: 24 minutes 46.68 seconds (1486.68 seconds total)