Starting phenix.real_space_refine on Mon Jun 9 08:23:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6o_36009/06_2025/8j6o_36009.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6o_36009/06_2025/8j6o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6o_36009/06_2025/8j6o_36009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6o_36009/06_2025/8j6o_36009.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6o_36009/06_2025/8j6o_36009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6o_36009/06_2025/8j6o_36009.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 4, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} 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: 7.20, per 1000 atoms: 0.69 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: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.21 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: 3.65 Time building geometry restraints manager: 3.51 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 \ 832 or resid 901 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 832 or \ resid 901 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: 21.550 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.460 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 55.920 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 320 HIS 0.004 0.001 HIS B 568 PHE 0.029 0.002 PHE A 576 TYR 0.025 0.002 TYR B 584 ARG 0.014 0.001 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00796 ( 8) link_NAG-ASN : angle 6.34388 ( 24) link_BETA1-4 : bond 0.01106 ( 4) link_BETA1-4 : angle 1.29926 ( 12) hydrogen bonds : bond 0.17742 ( 626) hydrogen bonds : angle 6.97227 ( 1806) metal coordination : bond 0.32655 ( 6) SS BOND : bond 0.00145 ( 8) SS BOND : angle 3.46123 ( 16) covalent geometry : bond 0.00603 (10690) covalent geometry : angle 1.02165 (14543) *********************** 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 : 1.100 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: 0.2162 (mmt) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.2097 time to fit residues: 57.4267 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 : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 0.0270 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 overall best weight: 1.7042 ------------------------------------------------------------------------------- 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 603 ASN B 699 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.199018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.139712 restraints weight = 10507.104| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.84 r_work: 0.3347 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 10716 Z= 0.249 Angle : 0.786 13.739 14595 Z= 0.390 Chirality : 0.053 0.439 1727 Planarity : 0.007 0.154 1809 Dihedral : 11.971 70.037 1653 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.11 % Rotamer: Outliers : 3.10 % Allowed : 18.41 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1284 helix: 1.73 (0.20), residues: 580 sheet: 0.65 (0.29), residues: 280 loop : -0.88 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 634 HIS 0.007 0.001 HIS A 796 PHE 0.039 0.002 PHE B 714 TYR 0.032 0.002 TYR A 584 ARG 0.005 0.001 ARG A 59 Details of bonding type rmsd link_NAG-ASN : bond 0.01071 ( 8) link_NAG-ASN : angle 5.85317 ( 24) link_BETA1-4 : bond 0.01127 ( 4) link_BETA1-4 : angle 2.68115 ( 12) hydrogen bonds : bond 0.05164 ( 626) hydrogen bonds : angle 5.50548 ( 1806) metal coordination : bond 0.01331 ( 6) SS BOND : bond 0.00287 ( 8) SS BOND : angle 1.60714 ( 16) covalent geometry : bond 0.00595 (10690) covalent geometry : angle 0.74521 (14543) *********************** 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 179 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: A 200 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8203 (mm) REVERT: A 562 LEU cc_start: 0.8136 (tp) cc_final: 0.7594 (mt) REVERT: A 689 MET cc_start: 0.2259 (mmt) cc_final: 0.1718 (mmt) REVERT: A 745 LYS cc_start: 0.6519 (mmmt) cc_final: 0.5920 (tttt) REVERT: A 815 LEU cc_start: 0.7772 (tp) cc_final: 0.7434 (mt) REVERT: A 816 THR cc_start: 0.8725 (p) cc_final: 0.8078 (t) REVERT: B 145 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: B 297 MET cc_start: 0.7436 (tpp) cc_final: 0.7218 (tpt) REVERT: B 551 TYR cc_start: 0.8039 (m-80) cc_final: 0.7834 (m-80) REVERT: B 562 LEU cc_start: 0.8124 (tp) cc_final: 0.7531 (mt) REVERT: B 597 LYS cc_start: 0.6363 (ptmt) cc_final: 0.6163 (ptpt) REVERT: B 689 MET cc_start: 0.2163 (mmt) cc_final: 0.1606 (mmt) REVERT: B 694 MET cc_start: 0.5566 (pmm) cc_final: 0.5248 (ppp) REVERT: B 816 THR cc_start: 0.8635 (p) cc_final: 0.8136 (t) REVERT: B 826 ARG cc_start: 0.8051 (tmm-80) cc_final: 0.7794 (tmt170) outliers start: 35 outliers final: 17 residues processed: 171 average time/residue: 0.2480 time to fit residues: 63.4550 Evaluate side-chains 146 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 145 GLN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 200 ILE 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 200 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 264 PRO Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 72 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 102 optimal weight: 9.9990 chunk 78 optimal weight: 0.0040 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.208482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152609 restraints weight = 10709.070| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.77 r_work: 0.3473 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 10716 Z= 0.141 Angle : 0.653 14.195 14595 Z= 0.319 Chirality : 0.047 0.389 1727 Planarity : 0.006 0.138 1809 Dihedral : 8.998 62.537 1653 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.73 % Favored : 97.12 % Rotamer: Outliers : 3.10 % Allowed : 19.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1284 helix: 1.92 (0.20), residues: 582 sheet: 0.65 (0.29), residues: 280 loop : -0.71 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 799 HIS 0.002 0.001 HIS B 800 PHE 0.017 0.001 PHE A 304 TYR 0.030 0.002 TYR A 584 ARG 0.013 0.001 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.01081 ( 8) link_NAG-ASN : angle 5.88392 ( 24) link_BETA1-4 : bond 0.00765 ( 4) link_BETA1-4 : angle 2.91616 ( 12) hydrogen bonds : bond 0.04429 ( 626) hydrogen bonds : angle 5.14497 ( 1806) metal coordination : bond 0.00245 ( 6) SS BOND : bond 0.00169 ( 8) SS BOND : angle 0.97115 ( 16) covalent geometry : bond 0.00322 (10690) covalent geometry : angle 0.60275 (14543) *********************** 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 176 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7778 (mt0) cc_final: 0.7469 (mt0) REVERT: A 233 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8644 (m) REVERT: A 496 ASN cc_start: 0.7009 (t0) cc_final: 0.6682 (t0) REVERT: A 562 LEU cc_start: 0.8178 (tp) cc_final: 0.7626 (mt) REVERT: A 689 MET cc_start: 0.2206 (mmt) cc_final: 0.2002 (mmt) REVERT: A 745 LYS cc_start: 0.6653 (mmmt) cc_final: 0.6018 (tttt) REVERT: A 807 MET cc_start: 0.7107 (mtp) cc_final: 0.6893 (mtp) REVERT: A 816 THR cc_start: 0.8846 (p) cc_final: 0.8344 (t) REVERT: B 145 GLN cc_start: 0.7961 (mt0) cc_final: 0.7568 (mt0) REVERT: B 522 GLN cc_start: 0.7456 (tm-30) cc_final: 0.7111 (tm-30) REVERT: B 560 GLU cc_start: 0.8428 (tp30) cc_final: 0.8191 (tp30) REVERT: B 597 LYS cc_start: 0.6392 (ptmt) cc_final: 0.6021 (ptmm) REVERT: B 689 MET cc_start: 0.2290 (mmt) cc_final: 0.2040 (mmt) REVERT: B 826 ARG cc_start: 0.8006 (tmm-80) cc_final: 0.7056 (tmt170) outliers start: 35 outliers final: 13 residues processed: 169 average time/residue: 0.2019 time to fit residues: 50.8946 Evaluate side-chains 143 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 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 652 LEU Chi-restraints excluded: chain B residue 29 SER 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 242 SER Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 3 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 97 optimal weight: 0.0870 chunk 79 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 24 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN 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 = 0.4368 r_free = 0.4368 target = 0.214395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.162320 restraints weight = 10833.777| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.36 r_work: 0.3516 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 10716 Z= 0.149 Angle : 0.633 14.158 14595 Z= 0.311 Chirality : 0.047 0.376 1727 Planarity : 0.005 0.126 1809 Dihedral : 8.078 58.664 1653 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.04 % Rotamer: Outliers : 3.45 % Allowed : 20.80 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.23), residues: 1284 helix: 1.86 (0.20), residues: 580 sheet: 0.80 (0.28), residues: 298 loop : -0.68 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 799 HIS 0.010 0.001 HIS B 492 PHE 0.027 0.002 PHE A 578 TYR 0.030 0.002 TYR A 584 ARG 0.004 0.000 ARG B 785 Details of bonding type rmsd link_NAG-ASN : bond 0.01097 ( 8) link_NAG-ASN : angle 5.78879 ( 24) link_BETA1-4 : bond 0.00755 ( 4) link_BETA1-4 : angle 2.71757 ( 12) hydrogen bonds : bond 0.04235 ( 626) hydrogen bonds : angle 4.96426 ( 1806) metal coordination : bond 0.00193 ( 6) SS BOND : bond 0.00319 ( 8) SS BOND : angle 1.22813 ( 16) covalent geometry : bond 0.00348 (10690) covalent geometry : angle 0.58281 (14543) *********************** 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 177 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7973 (mt0) cc_final: 0.7512 (mp10) REVERT: A 233 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8754 (m) REVERT: A 496 ASN cc_start: 0.7148 (t0) cc_final: 0.6838 (t0) REVERT: A 562 LEU cc_start: 0.8467 (tp) cc_final: 0.7893 (mt) REVERT: A 689 MET cc_start: 0.2277 (mmt) cc_final: 0.2028 (mmt) REVERT: A 745 LYS cc_start: 0.6824 (mmmt) cc_final: 0.6136 (tttt) REVERT: A 807 MET cc_start: 0.7408 (mtp) cc_final: 0.7049 (mtp) REVERT: B 63 GLU cc_start: 0.6826 (tt0) cc_final: 0.6396 (tp30) REVERT: B 145 GLN cc_start: 0.8067 (mt0) cc_final: 0.7680 (mp10) REVERT: B 496 ASN cc_start: 0.7146 (t0) cc_final: 0.6916 (t0) REVERT: B 522 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7299 (tm-30) REVERT: B 689 MET cc_start: 0.2299 (mmt) cc_final: 0.2094 (mmt) outliers start: 39 outliers final: 25 residues processed: 166 average time/residue: 0.2038 time to fit residues: 51.3541 Evaluate side-chains 154 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 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 569 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 LEU 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 242 SER 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 812 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 7 optimal weight: 0.0870 chunk 97 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 120 optimal weight: 0.0670 chunk 88 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.216668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.164449 restraints weight = 10827.551| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.43 r_work: 0.3544 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3388 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= 0.122 Angle : 0.613 13.722 14595 Z= 0.299 Chirality : 0.046 0.355 1727 Planarity : 0.005 0.119 1809 Dihedral : 7.589 53.963 1653 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.49 % Favored : 97.35 % Rotamer: Outliers : 3.10 % Allowed : 22.04 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.23), residues: 1284 helix: 1.88 (0.20), residues: 584 sheet: 0.86 (0.27), residues: 296 loop : -0.73 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 799 HIS 0.007 0.001 HIS A 492 PHE 0.038 0.002 PHE A 578 TYR 0.027 0.001 TYR A 584 ARG 0.003 0.000 ARG B 114 Details of bonding type rmsd link_NAG-ASN : bond 0.01057 ( 8) link_NAG-ASN : angle 5.85369 ( 24) link_BETA1-4 : bond 0.00677 ( 4) link_BETA1-4 : angle 2.79131 ( 12) hydrogen bonds : bond 0.04008 ( 626) hydrogen bonds : angle 4.83426 ( 1806) metal coordination : bond 0.00099 ( 6) SS BOND : bond 0.00261 ( 8) SS BOND : angle 1.26436 ( 16) covalent geometry : bond 0.00282 (10690) covalent geometry : angle 0.55846 (14543) *********************** 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 167 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.5361 (tp30) cc_final: 0.5015 (tm-30) REVERT: A 145 GLN cc_start: 0.8149 (mt0) cc_final: 0.7865 (mt0) REVERT: A 150 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7295 (ptt180) REVERT: A 496 ASN cc_start: 0.7134 (t0) cc_final: 0.6839 (t0) REVERT: A 562 LEU cc_start: 0.8457 (tp) cc_final: 0.7966 (mt) REVERT: A 745 LYS cc_start: 0.6754 (mmmt) cc_final: 0.6140 (ttpt) REVERT: B 63 GLU cc_start: 0.6629 (tt0) cc_final: 0.6145 (tp30) REVERT: B 145 GLN cc_start: 0.8110 (mt0) cc_final: 0.7805 (mt0) REVERT: B 496 ASN cc_start: 0.7168 (t0) cc_final: 0.6199 (t0) REVERT: B 522 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 743 ARG cc_start: 0.6814 (ttp-170) cc_final: 0.6028 (tpt170) outliers start: 35 outliers final: 19 residues processed: 158 average time/residue: 0.1868 time to fit residues: 44.4154 Evaluate side-chains 143 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 150 ARG Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 531 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 135 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.213946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.160492 restraints weight = 10782.568| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.67 r_work: 0.3515 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10716 Z= 0.146 Angle : 0.624 13.697 14595 Z= 0.305 Chirality : 0.047 0.346 1727 Planarity : 0.005 0.115 1809 Dihedral : 7.189 49.828 1653 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.73 % Favored : 97.12 % Rotamer: Outliers : 4.60 % Allowed : 20.62 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.23), residues: 1284 helix: 1.83 (0.20), residues: 582 sheet: 0.82 (0.27), residues: 298 loop : -0.71 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 799 HIS 0.004 0.001 HIS A 492 PHE 0.042 0.002 PHE A 578 TYR 0.026 0.001 TYR A 584 ARG 0.003 0.000 ARG A 147 Details of bonding type rmsd link_NAG-ASN : bond 0.01058 ( 8) link_NAG-ASN : angle 6.12927 ( 24) link_BETA1-4 : bond 0.00655 ( 4) link_BETA1-4 : angle 2.82211 ( 12) hydrogen bonds : bond 0.04086 ( 626) hydrogen bonds : angle 4.80474 ( 1806) metal coordination : bond 0.00228 ( 6) SS BOND : bond 0.00265 ( 8) SS BOND : angle 1.44369 ( 16) covalent geometry : bond 0.00345 (10690) covalent geometry : angle 0.56517 (14543) *********************** 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 175 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.8119 (mt0) cc_final: 0.7856 (mt0) REVERT: A 233 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8797 (m) REVERT: A 496 ASN cc_start: 0.7151 (t0) cc_final: 0.6323 (t0) REVERT: A 562 LEU cc_start: 0.8426 (tp) cc_final: 0.7923 (mt) REVERT: A 583 MET cc_start: 0.8271 (mmm) cc_final: 0.8062 (tpt) REVERT: A 689 MET cc_start: 0.2657 (mmt) cc_final: 0.2452 (mmm) REVERT: A 745 LYS cc_start: 0.6707 (mmmt) cc_final: 0.6060 (mtpt) REVERT: B 63 GLU cc_start: 0.6718 (tt0) cc_final: 0.6203 (tp30) REVERT: B 145 GLN cc_start: 0.8140 (mt0) cc_final: 0.7837 (mt0) REVERT: B 496 ASN cc_start: 0.7144 (t0) cc_final: 0.6150 (t0) REVERT: B 522 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 743 ARG cc_start: 0.6809 (ttp-170) cc_final: 0.5984 (tpt170) outliers start: 52 outliers final: 33 residues processed: 164 average time/residue: 0.1793 time to fit residues: 45.1131 Evaluate side-chains 147 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 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 316 CYS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 812 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 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 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 316 CYS Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 768 GLN Chi-restraints excluded: chain B residue 812 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 32 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.215435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.162362 restraints weight = 10919.041| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.42 r_work: 0.3517 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 10716 Z= 0.139 Angle : 0.631 13.622 14595 Z= 0.308 Chirality : 0.047 0.338 1727 Planarity : 0.005 0.112 1809 Dihedral : 6.928 49.254 1653 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.80 % Favored : 96.96 % Rotamer: Outliers : 3.89 % Allowed : 22.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.23), residues: 1284 helix: 1.84 (0.21), residues: 582 sheet: 0.88 (0.27), residues: 296 loop : -0.74 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 799 HIS 0.003 0.001 HIS A 492 PHE 0.036 0.002 PHE A 578 TYR 0.025 0.001 TYR A 584 ARG 0.005 0.000 ARG A 147 Details of bonding type rmsd link_NAG-ASN : bond 0.01046 ( 8) link_NAG-ASN : angle 6.20943 ( 24) link_BETA1-4 : bond 0.00745 ( 4) link_BETA1-4 : angle 2.72552 ( 12) hydrogen bonds : bond 0.04030 ( 626) hydrogen bonds : angle 4.77285 ( 1806) metal coordination : bond 0.00196 ( 6) SS BOND : bond 0.00210 ( 8) SS BOND : angle 1.27527 ( 16) covalent geometry : bond 0.00325 (10690) covalent geometry : angle 0.57239 (14543) *********************** 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 163 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.5072 (tp30) cc_final: 0.4494 (tm-30) REVERT: A 145 GLN cc_start: 0.8090 (mt0) cc_final: 0.7826 (mt0) REVERT: A 150 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7176 (ptm160) REVERT: A 225 MET cc_start: 0.8864 (ptm) cc_final: 0.8520 (ptm) REVERT: A 233 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8790 (m) REVERT: A 496 ASN cc_start: 0.7128 (t0) cc_final: 0.6141 (t0) REVERT: A 745 LYS cc_start: 0.6766 (mmmt) cc_final: 0.6117 (mtpt) REVERT: B 145 GLN cc_start: 0.8114 (mt0) cc_final: 0.7824 (mt0) REVERT: B 496 ASN cc_start: 0.7144 (t0) cc_final: 0.6188 (t0) REVERT: B 522 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 689 MET cc_start: 0.2130 (mmt) cc_final: 0.1830 (mmt) REVERT: B 743 ARG cc_start: 0.6828 (ttp-170) cc_final: 0.6030 (tpt170) outliers start: 44 outliers final: 29 residues processed: 155 average time/residue: 0.1888 time to fit residues: 44.2601 Evaluate side-chains 146 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 149 SER Chi-restraints excluded: chain A residue 150 ARG 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 531 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 35 PHE 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 242 SER Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 768 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.203036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148628 restraints weight = 10937.700| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.64 r_work: 0.3365 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 10716 Z= 0.363 Angle : 0.809 13.943 14595 Z= 0.407 Chirality : 0.054 0.337 1727 Planarity : 0.006 0.112 1809 Dihedral : 7.335 50.729 1653 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.89 % Favored : 95.87 % Rotamer: Outliers : 4.16 % Allowed : 22.12 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1284 helix: 1.27 (0.20), residues: 580 sheet: 0.72 (0.29), residues: 306 loop : -1.13 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 773 HIS 0.005 0.001 HIS B 599 PHE 0.040 0.003 PHE A 578 TYR 0.024 0.003 TYR B 485 ARG 0.005 0.001 ARG B 276 Details of bonding type rmsd link_NAG-ASN : bond 0.00833 ( 8) link_NAG-ASN : angle 6.43133 ( 24) link_BETA1-4 : bond 0.00691 ( 4) link_BETA1-4 : angle 2.47683 ( 12) hydrogen bonds : bond 0.04979 ( 626) hydrogen bonds : angle 5.17474 ( 1806) metal coordination : bond 0.00788 ( 6) SS BOND : bond 0.00539 ( 8) SS BOND : angle 2.89426 ( 16) covalent geometry : bond 0.00872 (10690) covalent geometry : angle 0.75743 (14543) *********************** 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 175 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 145 GLN cc_start: 0.8215 (mt0) cc_final: 0.7939 (mt0) REVERT: A 150 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7644 (ttm110) REVERT: A 562 LEU cc_start: 0.8369 (tp) cc_final: 0.7927 (mt) REVERT: A 745 LYS cc_start: 0.6951 (mmmt) cc_final: 0.6257 (mtpt) REVERT: B 145 GLN cc_start: 0.8223 (mt0) cc_final: 0.7924 (mt0) REVERT: B 522 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7656 (tm-30) outliers start: 47 outliers final: 36 residues processed: 162 average time/residue: 0.1994 time to fit residues: 47.7053 Evaluate side-chains 154 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 150 ARG 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 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 812 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 226 THR 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 520 ILE 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 728 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 52 optimal weight: 0.0470 chunk 123 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.206143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.155379 restraints weight = 10763.094| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.39 r_work: 0.3489 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10716 Z= 0.141 Angle : 0.683 13.793 14595 Z= 0.330 Chirality : 0.048 0.321 1727 Planarity : 0.005 0.109 1809 Dihedral : 6.772 48.569 1653 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.80 % Favored : 96.96 % Rotamer: Outliers : 2.65 % Allowed : 23.72 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1284 helix: 1.63 (0.21), residues: 586 sheet: 0.66 (0.28), residues: 306 loop : -0.97 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 799 HIS 0.009 0.001 HIS A 599 PHE 0.032 0.001 PHE A 578 TYR 0.025 0.001 TYR A 584 ARG 0.003 0.000 ARG B 688 Details of bonding type rmsd link_NAG-ASN : bond 0.01037 ( 8) link_NAG-ASN : angle 6.40648 ( 24) link_BETA1-4 : bond 0.00856 ( 4) link_BETA1-4 : angle 2.71167 ( 12) hydrogen bonds : bond 0.04123 ( 626) hydrogen bonds : angle 4.91503 ( 1806) metal coordination : bond 0.00255 ( 6) SS BOND : bond 0.00271 ( 8) SS BOND : angle 4.04556 ( 16) covalent geometry : bond 0.00325 (10690) covalent geometry : angle 0.61300 (14543) *********************** 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 145 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.5427 (tp30) cc_final: 0.5189 (tp30) REVERT: A 145 GLN cc_start: 0.8085 (mt0) cc_final: 0.7828 (mt0) REVERT: A 150 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7298 (ptm160) REVERT: A 496 ASN cc_start: 0.7231 (t0) cc_final: 0.6214 (t0) REVERT: A 745 LYS cc_start: 0.6927 (mmmt) cc_final: 0.6241 (mtpt) REVERT: B 145 GLN cc_start: 0.8152 (mt0) cc_final: 0.7849 (mt0) REVERT: B 522 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7572 (tm-30) REVERT: B 689 MET cc_start: 0.2484 (mmt) cc_final: 0.1932 (mmt) REVERT: B 743 ARG cc_start: 0.6679 (ttp-170) cc_final: 0.5941 (tpt170) outliers start: 30 outliers final: 28 residues processed: 138 average time/residue: 0.1845 time to fit residues: 38.5375 Evaluate side-chains 141 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 150 ARG Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 226 THR 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 768 GLN Chi-restraints excluded: chain A residue 812 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 294 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 717 TYR 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 24 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 123 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 117 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.211679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160120 restraints weight = 10900.948| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.40 r_work: 0.3532 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10716 Z= 0.132 Angle : 0.669 13.938 14595 Z= 0.321 Chirality : 0.047 0.314 1727 Planarity : 0.005 0.108 1809 Dihedral : 6.546 48.205 1653 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.35 % Favored : 96.42 % Rotamer: Outliers : 2.57 % Allowed : 23.72 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.23), residues: 1284 helix: 1.70 (0.21), residues: 586 sheet: 0.77 (0.28), residues: 304 loop : -0.95 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 799 HIS 0.008 0.001 HIS A 599 PHE 0.037 0.002 PHE A 766 TYR 0.025 0.001 TYR B 584 ARG 0.002 0.000 ARG B 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00997 ( 8) link_NAG-ASN : angle 6.15337 ( 24) link_BETA1-4 : bond 0.00746 ( 4) link_BETA1-4 : angle 2.53250 ( 12) hydrogen bonds : bond 0.03962 ( 626) hydrogen bonds : angle 4.79318 ( 1806) metal coordination : bond 0.00237 ( 6) SS BOND : bond 0.00237 ( 8) SS BOND : angle 3.19857 ( 16) covalent geometry : bond 0.00309 (10690) covalent geometry : angle 0.60792 (14543) ********************** 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 143 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.076 Fit side-chains REVERT: A 145 GLN cc_start: 0.8098 (mt0) cc_final: 0.7817 (mt0) REVERT: A 496 ASN cc_start: 0.7229 (t0) cc_final: 0.6204 (t0) REVERT: A 745 LYS cc_start: 0.6849 (mmmt) cc_final: 0.6119 (mtpt) REVERT: B 145 GLN cc_start: 0.8217 (mt0) cc_final: 0.7887 (mt0) REVERT: B 522 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 689 MET cc_start: 0.2152 (mmt) cc_final: 0.1705 (mmt) REVERT: B 743 ARG cc_start: 0.6590 (ttp-170) cc_final: 0.5796 (tpt170) outliers start: 29 outliers final: 27 residues processed: 137 average time/residue: 0.2137 time to fit residues: 44.3294 Evaluate side-chains 140 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 226 THR 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 768 GLN Chi-restraints excluded: chain A residue 812 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 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 294 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 717 TYR 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 6 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.0770 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.214782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.159955 restraints weight = 10911.499| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.57 r_work: 0.3513 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10716 Z= 0.134 Angle : 0.664 13.647 14595 Z= 0.319 Chirality : 0.047 0.310 1727 Planarity : 0.005 0.106 1809 Dihedral : 6.414 48.212 1653 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.19 % Favored : 96.57 % Rotamer: Outliers : 2.65 % Allowed : 23.72 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1284 helix: 1.77 (0.21), residues: 586 sheet: 0.80 (0.28), residues: 304 loop : -0.97 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 799 HIS 0.008 0.001 HIS A 599 PHE 0.027 0.001 PHE A 578 TYR 0.026 0.001 TYR A 584 ARG 0.011 0.000 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.01004 ( 8) link_NAG-ASN : angle 6.15622 ( 24) link_BETA1-4 : bond 0.00794 ( 4) link_BETA1-4 : angle 2.55695 ( 12) hydrogen bonds : bond 0.03894 ( 626) hydrogen bonds : angle 4.75661 ( 1806) metal coordination : bond 0.00231 ( 6) SS BOND : bond 0.00233 ( 8) SS BOND : angle 2.79928 ( 16) covalent geometry : bond 0.00313 (10690) covalent geometry : angle 0.60465 (14543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5262.34 seconds wall clock time: 92 minutes 41.38 seconds (5561.38 seconds total)