Starting phenix.real_space_refine on Wed Feb 4 11:19:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6o_36009/02_2026/8j6o_36009.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6o_36009/02_2026/8j6o_36009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j6o_36009/02_2026/8j6o_36009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6o_36009/02_2026/8j6o_36009.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j6o_36009/02_2026/8j6o_36009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6o_36009/02_2026/8j6o_36009.map" } resolution = 3.25 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= 0.004 sd= 0.112 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 Zn 2 6.06 5 S 67 5.16 5 C 6807 2.51 5 N 1676 2.21 5 O 1899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10451 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5113 Classifications: {'peptide': 648} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 18, 'TRANS': 625} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 5168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5168 Classifications: {'peptide': 648} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 18, 'TRANS': 625} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.46, per 1000 atoms: 0.24 Number of scatterers: 10451 At special positions: 0 Unit cell: (73.84, 96.72, 134.16, 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) Zn 2 29.99 S 67 16.00 O 1899 8.00 N 1676 7.00 C 6807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 570 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 787 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 901 " - " ASN A 123 " " NAG A 902 " - " ASN A 27 " " NAG B 901 " - " ASN B 123 " " NAG B 902 " - " ASN B 27 " " NAG D 1 " - " ASN A 54 " " NAG G 1 " - " ASN A 165 " " NAG J 1 " - " ASN B 54 " " NAG M 1 " - " ASN B 165 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 480.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 568 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 568 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 800 " 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 48.9% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 289 through 322 removed outlier: 3.820A pdb=" N TYR A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 304 " --> pdb=" O CYS A 300 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 479 Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.962A pdb=" N ILE A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 533 removed outlier: 3.976A pdb=" N ILE A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 541 Processing helix chain 'A' and resid 547 through 569 Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 575 through 599 removed outlier: 4.093A pdb=" N ASP A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N MET A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 594 " --> pdb=" O CYS A 590 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.543A pdb=" N SER A 605 " --> pdb=" O ILE A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 627 removed outlier: 3.666A pdb=" N VAL A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 622 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY A 623 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 655 Processing helix chain 'A' and resid 685 through 707 removed outlier: 3.530A pdb=" N TYR A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 740 Processing helix chain 'A' and resid 745 through 769 Processing helix chain 'A' and resid 776 through 781 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 794 through 817 Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'B' and resid 289 through 322 removed outlier: 3.820A pdb=" N TYR B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 304 " --> pdb=" O CYS B 300 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 479 Proline residue: B 463 - end of helix Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.962A pdb=" N ILE B 503 " --> pdb=" O ALA B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 533 removed outlier: 3.977A pdb=" N ILE B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 541 Processing helix chain 'B' and resid 547 through 569 Processing helix chain 'B' and resid 572 through 574 No H-bonds generated for 'chain 'B' and resid 572 through 574' Processing helix chain 'B' and resid 575 through 599 removed outlier: 4.093A pdb=" N ASP B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N MET B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 594 " --> pdb=" O CYS B 590 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR B 595 " --> pdb=" O MET B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 removed outlier: 3.543A pdb=" N SER B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 627 removed outlier: 3.667A pdb=" N VAL B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 622 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY B 623 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 655 Processing helix chain 'B' and resid 685 through 707 removed outlier: 3.529A pdb=" N TYR B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 740 Processing helix chain 'B' and resid 745 through 769 Processing helix chain 'B' and resid 776 through 781 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 794 through 817 Processing helix chain 'B' and resid 818 through 823 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 156 removed outlier: 4.408A pdb=" N GLU A 177 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 162 through 166 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 32 Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 43 Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 100 Processing sheet with id=AA9, first strand: chain 'B' and resid 155 through 156 removed outlier: 4.408A pdb=" N GLU B 177 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 162 through 166 626 hydrogen bonds defined for protein. 1806 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: 1.71 Time building geometry restraints manager: 1.07 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: 2673 1.33 - 1.46: 2421 1.46 - 1.58: 5494 1.58 - 1.70: 4 1.70 - 1.83: 98 Bond restraints: 10690 Sorted by residual: bond pdb=" N PRO A 264 " pdb=" CD PRO A 264 " ideal model delta sigma weight residual 1.473 1.663 -0.190 1.40e-02 5.10e+03 1.83e+02 bond pdb=" N PRO B 264 " pdb=" CD PRO B 264 " ideal model delta sigma weight residual 1.473 1.650 -0.177 1.40e-02 5.10e+03 1.60e+02 bond pdb=" N PRO B 25 " pdb=" CD PRO B 25 " ideal model delta sigma weight residual 1.473 1.612 -0.139 1.40e-02 5.10e+03 9.91e+01 bond pdb=" N PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 1.473 1.612 -0.139 1.40e-02 5.10e+03 9.84e+01 bond pdb=" C GLY A 706 " pdb=" N LEU A 707 " ideal model delta sigma weight residual 1.328 1.389 -0.061 1.42e-02 4.96e+03 1.82e+01 ... (remaining 10685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.27: 14483 5.27 - 10.55: 46 10.55 - 15.82: 8 15.82 - 21.10: 1 21.10 - 26.37: 5 Bond angle restraints: 14543 Sorted by residual: angle pdb=" N MET A 709 " pdb=" CA MET A 709 " pdb=" C MET A 709 " ideal model delta sigma weight residual 110.10 130.37 -20.27 1.49e+00 4.50e-01 1.85e+02 angle pdb=" N ILE A 708 " pdb=" CA ILE A 708 " pdb=" C ILE A 708 " ideal model delta sigma weight residual 109.34 82.97 26.37 2.08e+00 2.31e-01 1.61e+02 angle pdb=" N ILE B 708 " pdb=" CA ILE B 708 " pdb=" C ILE B 708 " ideal model delta sigma weight residual 109.34 83.02 26.32 2.08e+00 2.31e-01 1.60e+02 angle pdb=" N MET B 709 " pdb=" CA MET B 709 " pdb=" C MET B 709 " ideal model delta sigma weight residual 110.80 133.92 -23.12 2.13e+00 2.20e-01 1.18e+02 angle pdb=" N PRO A 711 " pdb=" CA PRO A 711 " pdb=" C PRO A 711 " ideal model delta sigma weight residual 113.53 99.69 13.84 1.39e+00 5.18e-01 9.92e+01 ... (remaining 14538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.47: 5813 20.47 - 40.93: 486 40.93 - 61.40: 91 61.40 - 81.86: 34 81.86 - 102.33: 38 Dihedral angle restraints: 6462 sinusoidal: 2638 harmonic: 3824 Sorted by residual: dihedral pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual 93.00 162.16 -69.16 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CB CYS B 117 " pdb=" SG CYS B 117 " pdb=" SG CYS B 207 " pdb=" CB CYS B 207 " ideal model delta sinusoidal sigma weight residual 93.00 162.11 -69.11 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" C MET A 709 " pdb=" N MET A 709 " pdb=" CA MET A 709 " pdb=" CB MET A 709 " ideal model delta harmonic sigma weight residual -122.60 -139.39 16.79 0 2.50e+00 1.60e-01 4.51e+01 ... (remaining 6459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 1689 0.189 - 0.378: 29 0.378 - 0.567: 2 0.567 - 0.756: 6 0.756 - 0.945: 1 Chirality restraints: 1727 Sorted by residual: chirality pdb=" CA MET A 709 " pdb=" N MET A 709 " pdb=" C MET A 709 " pdb=" CB MET A 709 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" CA MET B 709 " pdb=" N MET B 709 " pdb=" C MET B 709 " pdb=" CB MET B 709 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 123 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.65e+00 ... (remaining 1724 not shown) Planarity restraints: 1817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 263 " -0.170 5.00e-02 4.00e+02 2.38e-01 9.08e+01 pdb=" N PRO A 264 " 0.409 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " -0.155 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 263 " 0.165 5.00e-02 4.00e+02 2.33e-01 8.68e+01 pdb=" N PRO B 264 " -0.400 5.00e-02 4.00e+02 pdb=" CA PRO B 264 " 0.150 5.00e-02 4.00e+02 pdb=" CD PRO B 264 " 0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 706 " -0.041 2.00e-02 2.50e+03 8.59e-02 7.38e+01 pdb=" C GLY B 706 " 0.148 2.00e-02 2.50e+03 pdb=" O GLY B 706 " -0.060 2.00e-02 2.50e+03 pdb=" N LEU B 707 " -0.048 2.00e-02 2.50e+03 ... (remaining 1814 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 81 2.58 - 3.16: 8689 3.16 - 3.74: 16272 3.74 - 4.32: 22916 4.32 - 4.90: 37109 Nonbonded interactions: 85067 Sorted by model distance: nonbonded pdb=" NE2 GLN B 223 " pdb=" OE1 GLN B 481 " model vdw 1.999 3.120 nonbonded pdb=" NE2 GLN A 223 " pdb=" OE1 GLN A 481 " model vdw 2.000 3.120 nonbonded pdb=" O THR B 650 " pdb=" CD2 TYR B 654 " model vdw 2.008 3.340 nonbonded pdb=" OD1 ASP A 794 " pdb=" N ASP A 795 " model vdw 2.048 3.120 nonbonded pdb=" OD1 ASP B 794 " pdb=" N ASP B 795 " model vdw 2.049 3.120 ... (remaining 85062 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 25 through 266 or (resid 267 and (name N or name CA or nam \ e C or name O or name CB )) or resid 268 through 711 or (resid 712 and (name N o \ r name CA or name C or name O or name CB )) or resid 713 through 773 or (resid 7 \ 74 and (name N or name CA or name C or name O or name CB )) or resid 775 through \ 903)) selection = (chain 'B' and (resid 25 through 617 or (resid 618 through 619 and (name N or na \ me CA or name C or name O or name CB )) or resid 620 through 625 or (resid 626 a \ nd (name N or name CA or name C or name O or name CB )) or resid 627 or (resid 6 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 629 or (res \ id 630 and (name N or name CA or name C or name O or name CB )) or resid 631 thr \ ough 642 or (resid 643 through 644 and (name N or name CA or name C or name O or \ name CB )) or resid 645 through 646 or (resid 647 and (name N or name CA or nam \ e C or name O or name CB )) or resid 648 through 652 or (resid 653 through 654 a \ nd (name N or name CA or name C or name O or name CB )) or resid 655 through 693 \ or (resid 694 and (name N or name CA or name C or name O or name CB )) or resid \ 695 through 699 or (resid 700 and (name N or name CA or name C or name O or nam \ e CB )) or resid 701 through 707 or (resid 708 through 710 and (name N or name C \ A or name C or name O or name CB )) or resid 711 through 784 or (resid 785 and ( \ name N or name CA or name C or name O or name CB )) or resid 786 through 903)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.240 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 0.010 0.561 10716 Z= 0.470 Angle : 1.059 26.372 14595 Z= 0.616 Chirality : 0.075 0.945 1727 Planarity : 0.009 0.238 1809 Dihedral : 18.196 102.331 3966 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.10 % Favored : 97.43 % Rotamer: Outliers : 0.27 % Allowed : 18.94 % Favored : 80.80 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % 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: 1.18 (0.23), residues: 1284 helix: 1.94 (0.21), residues: 582 sheet: 1.08 (0.28), residues: 308 loop : -1.29 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 59 TYR 0.025 0.002 TYR B 584 PHE 0.029 0.002 PHE A 576 TRP 0.008 0.001 TRP A 320 HIS 0.004 0.001 HIS B 568 Details of bonding type rmsd covalent geometry : bond 0.00603 (10690) covalent geometry : angle 1.02165 (14543) SS BOND : bond 0.00145 ( 8) SS BOND : angle 3.46123 ( 16) hydrogen bonds : bond 0.17742 ( 626) hydrogen bonds : angle 6.97227 ( 1806) metal coordination : bond 0.32655 ( 6) link_BETA1-4 : bond 0.01106 ( 4) link_BETA1-4 : angle 1.29926 ( 12) link_NAG-ASN : bond 0.00796 ( 8) link_NAG-ASN : angle 6.34388 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 551 TYR cc_start: 0.7986 (m-80) cc_final: 0.7700 (m-80) REVERT: A 585 MET cc_start: 0.7060 (tmm) cc_final: 0.5994 (mtt) REVERT: A 689 MET cc_start: 0.2795 (mmp) cc_final: 0.2177 (mmt) REVERT: B 494 LEU cc_start: 0.8516 (tp) cc_final: 0.8278 (tt) REVERT: B 585 MET cc_start: 0.7152 (tmm) cc_final: 0.6002 (mtt) REVERT: B 689 MET cc_start: 0.2695 (mmp) cc_final: 0.2163 (mmt) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.0972 time to fit residues: 26.6893 Evaluate side-chains 133 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 286 GLN A 528 ASN A 699 ASN B 145 GLN B 528 ASN B 699 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.216509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.163256 restraints weight = 10755.471| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.23 r_work: 0.3627 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 10716 Z= 0.201 Angle : 0.749 13.614 14595 Z= 0.368 Chirality : 0.051 0.435 1727 Planarity : 0.007 0.154 1809 Dihedral : 12.054 70.344 1653 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.50 % Favored : 96.34 % Rotamer: Outliers : 3.01 % Allowed : 18.05 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.11 (0.23), residues: 1284 helix: 1.88 (0.20), residues: 580 sheet: 0.68 (0.29), residues: 280 loop : -0.82 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 114 TYR 0.032 0.002 TYR A 584 PHE 0.036 0.002 PHE B 714 TRP 0.016 0.002 TRP B 634 HIS 0.008 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00477 (10690) covalent geometry : angle 0.70505 (14543) SS BOND : bond 0.00240 ( 8) SS BOND : angle 1.48198 ( 16) hydrogen bonds : bond 0.04856 ( 626) hydrogen bonds : angle 5.43376 ( 1806) metal coordination : bond 0.02645 ( 6) link_BETA1-4 : bond 0.00995 ( 4) link_BETA1-4 : angle 2.71265 ( 12) link_NAG-ASN : bond 0.01027 ( 8) link_NAG-ASN : angle 5.87026 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: A 225 MET cc_start: 0.8688 (ptm) cc_final: 0.8462 (ptm) REVERT: A 297 MET cc_start: 0.7682 (tpp) cc_final: 0.7392 (tpt) REVERT: A 494 LEU cc_start: 0.8468 (tp) cc_final: 0.8203 (tt) REVERT: A 551 TYR cc_start: 0.8130 (m-80) cc_final: 0.7771 (m-80) REVERT: A 689 MET cc_start: 0.2420 (mmt) cc_final: 0.2112 (mmt) REVERT: A 745 LYS cc_start: 0.6779 (mmmt) cc_final: 0.6303 (tttt) REVERT: B 105 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7685 (tpt-90) REVERT: B 145 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: B 233 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8653 (m) REVERT: B 551 TYR cc_start: 0.7975 (m-80) cc_final: 0.7735 (m-80) REVERT: B 562 LEU cc_start: 0.8463 (tp) cc_final: 0.7892 (mt) REVERT: B 689 MET cc_start: 0.2263 (mmt) cc_final: 0.1626 (mmt) REVERT: B 694 MET cc_start: 0.5571 (pmm) cc_final: 0.5215 (ppp) REVERT: B 792 PHE cc_start: 0.8256 (t80) cc_final: 0.8025 (t80) REVERT: B 826 ARG cc_start: 0.7974 (tmm-80) cc_final: 0.7026 (tmt170) outliers start: 34 outliers final: 13 residues processed: 171 average time/residue: 0.0924 time to fit residues: 23.3497 Evaluate side-chains 144 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 264 PRO Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 264 PRO Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153808 restraints weight = 10888.863| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.62 r_work: 0.3474 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10716 Z= 0.208 Angle : 0.696 14.289 14595 Z= 0.345 Chirality : 0.049 0.393 1727 Planarity : 0.006 0.138 1809 Dihedral : 8.999 62.981 1653 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.73 % Rotamer: Outliers : 3.63 % Allowed : 19.12 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.01 (0.23), residues: 1284 helix: 1.77 (0.20), residues: 576 sheet: 0.60 (0.28), residues: 280 loop : -0.78 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 59 TYR 0.030 0.002 TYR A 584 PHE 0.031 0.002 PHE B 578 TRP 0.010 0.001 TRP A 799 HIS 0.004 0.001 HIS B 800 Details of bonding type rmsd covalent geometry : bond 0.00492 (10690) covalent geometry : angle 0.65054 (14543) SS BOND : bond 0.00248 ( 8) SS BOND : angle 1.25865 ( 16) hydrogen bonds : bond 0.04731 ( 626) hydrogen bonds : angle 5.19282 ( 1806) metal coordination : bond 0.00257 ( 6) link_BETA1-4 : bond 0.00754 ( 4) link_BETA1-4 : angle 2.79640 ( 12) link_NAG-ASN : bond 0.00944 ( 8) link_NAG-ASN : angle 5.79577 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.8439 (t) cc_final: 0.8219 (p) REVERT: A 225 MET cc_start: 0.8792 (ptm) cc_final: 0.8574 (ptm) REVERT: A 233 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8751 (m) REVERT: A 496 ASN cc_start: 0.7095 (t0) cc_final: 0.6782 (t0) REVERT: A 562 LEU cc_start: 0.8362 (tp) cc_final: 0.7832 (mt) REVERT: A 689 MET cc_start: 0.2193 (mmt) cc_final: 0.1993 (mmt) REVERT: A 745 LYS cc_start: 0.6752 (mmmt) cc_final: 0.6140 (tttt) REVERT: A 807 MET cc_start: 0.7385 (mtp) cc_final: 0.7136 (mtp) REVERT: A 815 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7639 (mp) REVERT: B 50 ILE cc_start: 0.8230 (mm) cc_final: 0.7923 (mt) REVERT: B 145 GLN cc_start: 0.7971 (mt0) cc_final: 0.7756 (mt0) REVERT: B 233 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8805 (m) REVERT: B 562 LEU cc_start: 0.8245 (tp) cc_final: 0.7718 (mt) REVERT: B 689 MET cc_start: 0.2316 (mmt) cc_final: 0.1695 (mmt) REVERT: B 826 ARG cc_start: 0.8066 (tmm-80) cc_final: 0.7057 (tmt170) outliers start: 41 outliers final: 21 residues processed: 171 average time/residue: 0.0843 time to fit residues: 21.6545 Evaluate side-chains 152 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 73 ASN B 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.208277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156669 restraints weight = 10888.752| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.56 r_work: 0.3511 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10716 Z= 0.159 Angle : 0.638 14.095 14595 Z= 0.315 Chirality : 0.047 0.376 1727 Planarity : 0.005 0.127 1809 Dihedral : 8.153 59.461 1653 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.20 % Rotamer: Outliers : 4.16 % Allowed : 20.27 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.15 (0.23), residues: 1284 helix: 1.86 (0.20), residues: 576 sheet: 0.65 (0.27), residues: 298 loop : -0.71 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 785 TYR 0.029 0.001 TYR A 584 PHE 0.038 0.002 PHE B 578 TRP 0.013 0.001 TRP A 799 HIS 0.011 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00375 (10690) covalent geometry : angle 0.58870 (14543) SS BOND : bond 0.00194 ( 8) SS BOND : angle 1.16629 ( 16) hydrogen bonds : bond 0.04347 ( 626) hydrogen bonds : angle 5.00082 ( 1806) metal coordination : bond 0.00227 ( 6) link_BETA1-4 : bond 0.00586 ( 4) link_BETA1-4 : angle 2.63503 ( 12) link_NAG-ASN : bond 0.01046 ( 8) link_NAG-ASN : angle 5.78398 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8730 (m) REVERT: A 496 ASN cc_start: 0.7173 (t0) cc_final: 0.6885 (t0) REVERT: A 562 LEU cc_start: 0.8293 (tp) cc_final: 0.7743 (mt) REVERT: A 689 MET cc_start: 0.2251 (mmt) cc_final: 0.1997 (mmt) REVERT: A 745 LYS cc_start: 0.6771 (mmmt) cc_final: 0.6121 (tttt) REVERT: A 807 MET cc_start: 0.7320 (mtp) cc_final: 0.6982 (mtp) REVERT: B 63 GLU cc_start: 0.6687 (tt0) cc_final: 0.6343 (tp30) REVERT: B 145 GLN cc_start: 0.8087 (mt0) cc_final: 0.7730 (mt0) REVERT: B 233 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8747 (m) REVERT: B 496 ASN cc_start: 0.7050 (t0) cc_final: 0.6816 (t0) REVERT: B 522 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7225 (tm-30) REVERT: B 689 MET cc_start: 0.2310 (mmt) cc_final: 0.2087 (mmt) outliers start: 47 outliers final: 28 residues processed: 169 average time/residue: 0.0797 time to fit residues: 20.6199 Evaluate side-chains 156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 756 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 87 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 796 HIS ** 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 = 0.4369 r_free = 0.4369 target = 0.214450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161007 restraints weight = 10850.686| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.48 r_work: 0.3513 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 10716 Z= 0.140 Angle : 0.621 13.824 14595 Z= 0.306 Chirality : 0.047 0.362 1727 Planarity : 0.005 0.120 1809 Dihedral : 7.705 54.927 1653 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.20 % Rotamer: Outliers : 4.07 % Allowed : 20.97 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.22 (0.23), residues: 1284 helix: 1.93 (0.20), residues: 580 sheet: 0.71 (0.27), residues: 298 loop : -0.73 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 114 TYR 0.028 0.001 TYR A 584 PHE 0.036 0.002 PHE B 578 TRP 0.012 0.001 TRP A 799 HIS 0.007 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00330 (10690) covalent geometry : angle 0.56823 (14543) SS BOND : bond 0.00247 ( 8) SS BOND : angle 1.18886 ( 16) hydrogen bonds : bond 0.04124 ( 626) hydrogen bonds : angle 4.87671 ( 1806) metal coordination : bond 0.00175 ( 6) link_BETA1-4 : bond 0.00672 ( 4) link_BETA1-4 : angle 2.65335 ( 12) link_NAG-ASN : bond 0.01045 ( 8) link_NAG-ASN : angle 5.87377 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8781 (m) REVERT: A 496 ASN cc_start: 0.7179 (t0) cc_final: 0.6910 (t0) REVERT: A 562 LEU cc_start: 0.8454 (tp) cc_final: 0.7893 (mt) REVERT: A 745 LYS cc_start: 0.6782 (mmmt) cc_final: 0.6155 (ttpt) REVERT: B 63 GLU cc_start: 0.6696 (tt0) cc_final: 0.6190 (tp30) REVERT: B 145 GLN cc_start: 0.8158 (mt0) cc_final: 0.7883 (mt0) REVERT: B 233 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8787 (m) REVERT: B 496 ASN cc_start: 0.7215 (t0) cc_final: 0.6966 (t0) REVERT: B 522 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7465 (tm-30) outliers start: 46 outliers final: 34 residues processed: 162 average time/residue: 0.0795 time to fit residues: 19.9813 Evaluate side-chains 156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 4.9990 chunk 65 optimal weight: 0.0670 chunk 37 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.213655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.159081 restraints weight = 10983.069| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.55 r_work: 0.3499 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10716 Z= 0.152 Angle : 0.620 13.720 14595 Z= 0.306 Chirality : 0.047 0.348 1727 Planarity : 0.005 0.117 1809 Dihedral : 7.276 50.106 1653 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.73 % Favored : 97.12 % Rotamer: Outliers : 4.60 % Allowed : 20.80 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.20 (0.23), residues: 1284 helix: 1.90 (0.21), residues: 582 sheet: 0.73 (0.27), residues: 298 loop : -0.76 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 114 TYR 0.026 0.001 TYR A 584 PHE 0.030 0.002 PHE B 578 TRP 0.010 0.001 TRP A 799 HIS 0.005 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00363 (10690) covalent geometry : angle 0.56364 (14543) SS BOND : bond 0.00525 ( 8) SS BOND : angle 1.59287 ( 16) hydrogen bonds : bond 0.04103 ( 626) hydrogen bonds : angle 4.83890 ( 1806) metal coordination : bond 0.00241 ( 6) link_BETA1-4 : bond 0.00678 ( 4) link_BETA1-4 : angle 2.73703 ( 12) link_NAG-ASN : bond 0.01056 ( 8) link_NAG-ASN : angle 6.00319 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 117 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.5139 (tm-30) cc_final: 0.4753 (tm-30) REVERT: A 150 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7222 (ptm160) REVERT: A 233 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8830 (m) REVERT: A 496 ASN cc_start: 0.7240 (t0) cc_final: 0.6941 (t0) REVERT: A 689 MET cc_start: 0.2623 (mmt) cc_final: 0.2418 (mmm) REVERT: A 745 LYS cc_start: 0.6836 (mmmt) cc_final: 0.6179 (mtpt) REVERT: B 145 GLN cc_start: 0.8173 (mt0) cc_final: 0.7894 (mt0) REVERT: B 233 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8830 (m) REVERT: B 522 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 743 ARG cc_start: 0.6789 (ttp-170) cc_final: 0.5971 (tpt170) outliers start: 52 outliers final: 33 residues processed: 158 average time/residue: 0.0843 time to fit residues: 20.2581 Evaluate side-chains 147 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 6 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.211388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158610 restraints weight = 10800.640| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.38 r_work: 0.3478 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10716 Z= 0.188 Angle : 0.655 13.736 14595 Z= 0.321 Chirality : 0.048 0.341 1727 Planarity : 0.005 0.114 1809 Dihedral : 7.108 50.015 1653 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.35 % Favored : 96.42 % Rotamer: Outliers : 5.04 % Allowed : 20.97 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.09 (0.23), residues: 1284 helix: 1.83 (0.21), residues: 578 sheet: 0.73 (0.28), residues: 298 loop : -0.88 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 59 TYR 0.026 0.002 TYR A 584 PHE 0.028 0.002 PHE B 578 TRP 0.008 0.001 TRP A 799 HIS 0.008 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00449 (10690) covalent geometry : angle 0.59295 (14543) SS BOND : bond 0.00280 ( 8) SS BOND : angle 1.53383 ( 16) hydrogen bonds : bond 0.04224 ( 626) hydrogen bonds : angle 4.87471 ( 1806) metal coordination : bond 0.00348 ( 6) link_BETA1-4 : bond 0.00648 ( 4) link_BETA1-4 : angle 2.72043 ( 12) link_NAG-ASN : bond 0.00988 ( 8) link_NAG-ASN : angle 6.52305 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 119 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 233 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8847 (m) REVERT: A 496 ASN cc_start: 0.7235 (t0) cc_final: 0.6971 (t0) REVERT: A 689 MET cc_start: 0.2567 (mmt) cc_final: 0.2190 (mmt) REVERT: A 745 LYS cc_start: 0.6896 (mmmt) cc_final: 0.6234 (mtpt) REVERT: B 145 GLN cc_start: 0.8174 (mt0) cc_final: 0.7919 (mt0) REVERT: B 233 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8835 (m) REVERT: B 496 ASN cc_start: 0.7417 (t0) cc_final: 0.6682 (t0) REVERT: B 522 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7505 (tm-30) REVERT: B 689 MET cc_start: 0.2157 (mmt) cc_final: 0.0923 (mmt) REVERT: B 743 ARG cc_start: 0.6834 (ttp-170) cc_final: 0.6095 (tpt170) outliers start: 57 outliers final: 39 residues processed: 162 average time/residue: 0.0847 time to fit residues: 21.0161 Evaluate side-chains 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0270 chunk 120 optimal weight: 0.0270 chunk 32 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 599 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.211227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158313 restraints weight = 10917.081| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.39 r_work: 0.3472 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10716 Z= 0.185 Angle : 0.677 13.760 14595 Z= 0.332 Chirality : 0.048 0.334 1727 Planarity : 0.005 0.112 1809 Dihedral : 6.975 49.634 1653 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.50 % Favored : 96.26 % Rotamer: Outliers : 4.34 % Allowed : 21.59 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.23), residues: 1284 helix: 1.73 (0.21), residues: 586 sheet: 0.66 (0.28), residues: 298 loop : -0.96 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 150 TYR 0.025 0.002 TYR A 584 PHE 0.032 0.002 PHE A 578 TRP 0.012 0.001 TRP B 773 HIS 0.027 0.002 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00439 (10690) covalent geometry : angle 0.61267 (14543) SS BOND : bond 0.00477 ( 8) SS BOND : angle 3.05046 ( 16) hydrogen bonds : bond 0.04248 ( 626) hydrogen bonds : angle 4.89465 ( 1806) metal coordination : bond 0.00359 ( 6) link_BETA1-4 : bond 0.00799 ( 4) link_BETA1-4 : angle 2.64599 ( 12) link_NAG-ASN : bond 0.00977 ( 8) link_NAG-ASN : angle 6.46092 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.5327 (tm-30) cc_final: 0.4628 (tm-30) REVERT: A 233 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8853 (m) REVERT: A 496 ASN cc_start: 0.7249 (t0) cc_final: 0.6981 (t0) REVERT: A 745 LYS cc_start: 0.6862 (mmmt) cc_final: 0.6198 (mtpt) REVERT: B 145 GLN cc_start: 0.8184 (mt0) cc_final: 0.7900 (mt0) REVERT: B 233 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8832 (m) REVERT: B 496 ASN cc_start: 0.7465 (t0) cc_final: 0.6682 (t0) REVERT: B 522 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7508 (tm-30) REVERT: B 689 MET cc_start: 0.1645 (mmt) cc_final: 0.1098 (mmt) REVERT: B 743 ARG cc_start: 0.6814 (ttp-170) cc_final: 0.6057 (tpt170) outliers start: 49 outliers final: 43 residues processed: 147 average time/residue: 0.0880 time to fit residues: 19.4660 Evaluate side-chains 152 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 599 HIS Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN B 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.202970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151924 restraints weight = 10724.936| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.53 r_work: 0.3449 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 10716 Z= 0.211 Angle : 0.684 13.791 14595 Z= 0.338 Chirality : 0.049 0.330 1727 Planarity : 0.005 0.111 1809 Dihedral : 6.879 49.322 1653 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.58 % Favored : 96.18 % Rotamer: Outliers : 4.42 % Allowed : 21.50 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.23), residues: 1284 helix: 1.71 (0.21), residues: 582 sheet: 0.58 (0.28), residues: 298 loop : -0.98 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 157 TYR 0.024 0.002 TYR B 584 PHE 0.050 0.002 PHE A 578 TRP 0.007 0.001 TRP B 634 HIS 0.014 0.001 HIS B 599 Details of bonding type rmsd covalent geometry : bond 0.00504 (10690) covalent geometry : angle 0.62346 (14543) SS BOND : bond 0.00417 ( 8) SS BOND : angle 2.51391 ( 16) hydrogen bonds : bond 0.04344 ( 626) hydrogen bonds : angle 4.93140 ( 1806) metal coordination : bond 0.00422 ( 6) link_BETA1-4 : bond 0.00724 ( 4) link_BETA1-4 : angle 2.55272 ( 12) link_NAG-ASN : bond 0.00963 ( 8) link_NAG-ASN : angle 6.46084 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 233 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8856 (m) REVERT: A 496 ASN cc_start: 0.7326 (t0) cc_final: 0.7052 (t0) REVERT: A 583 MET cc_start: 0.8323 (mmm) cc_final: 0.8091 (tpt) REVERT: A 689 MET cc_start: 0.1845 (mmt) cc_final: 0.1584 (mmt) REVERT: A 745 LYS cc_start: 0.6943 (mmmt) cc_final: 0.6252 (mtpt) REVERT: B 145 GLN cc_start: 0.8203 (mt0) cc_final: 0.7902 (mt0) REVERT: B 233 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8831 (m) REVERT: B 496 ASN cc_start: 0.7515 (t0) cc_final: 0.7028 (t0) REVERT: B 522 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 689 MET cc_start: 0.1655 (mmt) cc_final: 0.1099 (mmt) REVERT: B 743 ARG cc_start: 0.6786 (ttp-170) cc_final: 0.6089 (tpt170) outliers start: 50 outliers final: 42 residues processed: 152 average time/residue: 0.0857 time to fit residues: 19.8051 Evaluate side-chains 156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 0.0370 chunk 11 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 HIS B 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.205160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.154535 restraints weight = 10627.805| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.50 r_work: 0.3482 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10716 Z= 0.154 Angle : 0.661 13.749 14595 Z= 0.323 Chirality : 0.047 0.320 1727 Planarity : 0.005 0.109 1809 Dihedral : 6.611 48.422 1653 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.19 % Favored : 96.57 % Rotamer: Outliers : 3.98 % Allowed : 22.04 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.02 (0.23), residues: 1284 helix: 1.82 (0.21), residues: 586 sheet: 0.69 (0.28), residues: 290 loop : -1.02 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 150 TYR 0.025 0.001 TYR A 584 PHE 0.041 0.002 PHE A 578 TRP 0.010 0.001 TRP B 799 HIS 0.008 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00363 (10690) covalent geometry : angle 0.59499 (14543) SS BOND : bond 0.00375 ( 8) SS BOND : angle 3.35785 ( 16) hydrogen bonds : bond 0.04068 ( 626) hydrogen bonds : angle 4.82627 ( 1806) metal coordination : bond 0.00234 ( 6) link_BETA1-4 : bond 0.00728 ( 4) link_BETA1-4 : angle 2.57651 ( 12) link_NAG-ASN : bond 0.00989 ( 8) link_NAG-ASN : angle 6.32969 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8803 (m) REVERT: A 496 ASN cc_start: 0.7343 (t0) cc_final: 0.7075 (t0) REVERT: A 583 MET cc_start: 0.8344 (mmm) cc_final: 0.8080 (tpt) REVERT: A 689 MET cc_start: 0.1446 (mmt) cc_final: 0.1219 (mmt) REVERT: A 745 LYS cc_start: 0.6919 (mmmt) cc_final: 0.6224 (mtpt) REVERT: B 145 GLN cc_start: 0.8230 (mt0) cc_final: 0.7954 (mt0) REVERT: B 233 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8785 (m) REVERT: B 496 ASN cc_start: 0.7495 (t0) cc_final: 0.6729 (t0) REVERT: B 522 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7530 (tm-30) REVERT: B 743 ARG cc_start: 0.6659 (ttp-170) cc_final: 0.5930 (tpt170) outliers start: 45 outliers final: 40 residues processed: 143 average time/residue: 0.0944 time to fit residues: 20.3445 Evaluate side-chains 149 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 599 HIS Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 756 SER Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 89 optimal weight: 0.0570 chunk 122 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 HIS B 599 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.206336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153440 restraints weight = 10833.303| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.58 r_work: 0.3439 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10716 Z= 0.181 Angle : 0.665 13.758 14595 Z= 0.327 Chirality : 0.048 0.318 1727 Planarity : 0.005 0.108 1809 Dihedral : 6.555 48.685 1653 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.74 % Favored : 96.03 % Rotamer: Outliers : 3.89 % Allowed : 22.30 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.23), residues: 1284 helix: 1.80 (0.21), residues: 586 sheet: 0.67 (0.28), residues: 290 loop : -1.07 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 598 TYR 0.025 0.001 TYR B 584 PHE 0.044 0.002 PHE A 578 TRP 0.007 0.001 TRP A 634 HIS 0.014 0.001 HIS B 599 Details of bonding type rmsd covalent geometry : bond 0.00432 (10690) covalent geometry : angle 0.60359 (14543) SS BOND : bond 0.00364 ( 8) SS BOND : angle 3.09931 ( 16) hydrogen bonds : bond 0.04138 ( 626) hydrogen bonds : angle 4.82798 ( 1806) metal coordination : bond 0.00327 ( 6) link_BETA1-4 : bond 0.00774 ( 4) link_BETA1-4 : angle 2.48756 ( 12) link_NAG-ASN : bond 0.00953 ( 8) link_NAG-ASN : angle 6.19622 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2489.74 seconds wall clock time: 43 minutes 40.38 seconds (2620.38 seconds total)