Starting phenix.real_space_refine on Mon Jul 28 22:40:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wos_37697/07_2025/8wos_37697_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wos_37697/07_2025/8wos_37697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wos_37697/07_2025/8wos_37697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wos_37697/07_2025/8wos_37697.map" model { file = "/net/cci-nas-00/data/ceres_data/8wos_37697/07_2025/8wos_37697_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wos_37697/07_2025/8wos_37697_neut.cif" } resolution = 3.37 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= 0.000 sd= 0.013 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 58 5.16 5 C 7106 2.51 5 N 1644 2.21 5 O 1862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10672 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 Chain: "B" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 Chain: "C" 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: "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: "E" 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: "F" 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: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.09, per 1000 atoms: 0.76 Number of scatterers: 10672 At special positions: 0 Unit cell: (97.865, 86.802, 137.011, 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 58 16.00 O 1862 8.00 N 1644 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 67 " " NAG A 902 " - " ASN A 136 " " NAG B 901 " - " ASN B 67 " " NAG B 902 " - " ASN B 136 " " NAG C 1 " - " ASN A 83 " " NAG D 1 " - " ASN A 57 " " NAG E 1 " - " ASN B 83 " " NAG F 1 " - " ASN B 57 " Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 907 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 907 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 800 " 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 50.8% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 302 through 336 removed outlier: 3.884A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 474 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.941A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 501 through 529 removed outlier: 3.863A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.602A pdb=" N GLU A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 3.609A pdb=" N TYR A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 4.228A pdb=" N PHE A 571 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 594 removed outlier: 3.748A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 622 removed outlier: 3.922A pdb=" N TYR A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 649 Processing helix chain 'A' and resid 689 through 709 Processing helix chain 'A' and resid 713 through 740 Processing helix chain 'A' and resid 745 through 768 removed outlier: 3.667A pdb=" N GLN A 768 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 794 through 817 Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'B' and resid 38 through 43 Processing helix chain 'B' and resid 302 through 336 removed outlier: 3.866A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 474 removed outlier: 3.564A pdb=" N VAL B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 482 through 486 removed outlier: 4.030A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 529 removed outlier: 3.833A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 508 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.637A pdb=" N GLU B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 removed outlier: 3.522A pdb=" N TYR B 546 " --> pdb=" O PHE B 542 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N CYS B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.872A pdb=" N PHE B 571 " --> pdb=" O TYR B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 3.926A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 621 removed outlier: 3.660A pdb=" N TYR B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 649 Processing helix chain 'B' and resid 689 through 709 Processing helix chain 'B' and resid 713 through 740 Processing helix chain 'B' and resid 745 through 768 removed outlier: 3.524A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 768 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 782 Processing helix chain 'B' and resid 794 through 817 Processing helix chain 'B' and resid 818 through 822 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 removed outlier: 4.739A pdb=" N LYS A 192 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 178 through 181 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 70 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA9, first strand: chain 'B' and resid 170 through 171 removed outlier: 4.919A pdb=" N LYS B 192 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 181 615 hydrogen bonds defined for protein. 1758 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: 3.95 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3170 1.34 - 1.46: 2808 1.46 - 1.58: 4908 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 10976 Sorted by residual: bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 ... (remaining 10971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 14591 1.55 - 3.10: 339 3.10 - 4.65: 45 4.65 - 6.20: 1 6.20 - 7.75: 4 Bond angle restraints: 14980 Sorted by residual: angle pdb=" C SER B 600 " pdb=" CA SER B 600 " pdb=" CB SER B 600 " ideal model delta sigma weight residual 116.54 110.30 6.24 1.15e+00 7.56e-01 2.94e+01 angle pdb=" C LEU A 789 " pdb=" CA LEU A 789 " pdb=" CB LEU A 789 " ideal model delta sigma weight residual 116.63 111.62 5.01 1.16e+00 7.43e-01 1.87e+01 angle pdb=" CA SER B 600 " pdb=" C SER B 600 " pdb=" N ALA B 601 " ideal model delta sigma weight residual 119.52 116.43 3.09 7.90e-01 1.60e+00 1.53e+01 angle pdb=" C LEU A 704 " pdb=" N PHE A 705 " pdb=" CA PHE A 705 " ideal model delta sigma weight residual 122.06 114.81 7.25 1.86e+00 2.89e-01 1.52e+01 angle pdb=" C LEU B 789 " pdb=" CA LEU B 789 " pdb=" CB LEU B 789 " ideal model delta sigma weight residual 117.23 112.78 4.45 1.36e+00 5.41e-01 1.07e+01 ... (remaining 14975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 6322 25.77 - 51.54: 518 51.54 - 77.30: 55 77.30 - 103.07: 23 103.07 - 128.84: 10 Dihedral angle restraints: 6928 sinusoidal: 3148 harmonic: 3780 Sorted by residual: dihedral pdb=" CB CYS A 212 " pdb=" SG CYS A 212 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual 93.00 128.21 -35.21 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" C2 NAG B 901 " pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " pdb=" C5 NAG B 901 " ideal model delta sinusoidal sigma weight residual -62.96 65.88 -128.84 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual -62.96 65.20 -128.16 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1612 0.074 - 0.149: 135 0.149 - 0.223: 3 0.223 - 0.298: 0 0.298 - 0.372: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 1749 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 83 " 0.001 2.00e-02 2.50e+03 2.76e-02 9.53e+00 pdb=" CG ASN B 83 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 83 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN B 83 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 702 " -0.024 2.00e-02 2.50e+03 2.16e-02 8.15e+00 pdb=" CG PHE A 702 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 702 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 702 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 702 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 702 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 702 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 717 " -0.023 2.00e-02 2.50e+03 1.43e-02 4.10e+00 pdb=" CG TYR A 717 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 717 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 717 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 717 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 717 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 717 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 717 " -0.007 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 98 2.53 - 3.13: 8838 3.13 - 3.72: 16130 3.72 - 4.31: 21203 4.31 - 4.90: 36523 Nonbonded interactions: 82792 Sorted by model distance: nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 1.943 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 1.961 3.040 nonbonded pdb=" OG SER B 701 " pdb=" OH TYR B 717 " model vdw 1.981 3.040 nonbonded pdb=" OG SER A 740 " pdb=" OE2 GLU A 742 " model vdw 2.036 3.040 nonbonded pdb=" OH TYR A 321 " pdb=" O LEU A 506 " model vdw 2.086 3.040 ... (remaining 82787 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 35.700 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.140 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.003 0.053 11000 Z= 0.156 Angle : 0.590 10.534 15028 Z= 0.308 Chirality : 0.041 0.372 1752 Planarity : 0.003 0.049 1802 Dihedral : 18.351 128.840 4470 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 39.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.35 % Allowed : 33.39 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 1.07 (0.25), residues: 1256 helix: 2.71 (0.21), residues: 568 sheet: 0.51 (0.33), residues: 272 loop : -2.17 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 446 HIS 0.005 0.001 HIS B 636 PHE 0.050 0.001 PHE A 702 TYR 0.032 0.001 TYR A 717 ARG 0.001 0.000 ARG A 785 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 8) link_NAG-ASN : angle 5.10714 ( 24) link_BETA1-4 : bond 0.00198 ( 4) link_BETA1-4 : angle 1.52023 ( 12) hydrogen bonds : bond 0.10129 ( 615) hydrogen bonds : angle 4.85068 ( 1758) metal coordination : bond 0.00167 ( 6) SS BOND : bond 0.00186 ( 6) SS BOND : angle 1.09562 ( 12) covalent geometry : bond 0.00316 (10976) covalent geometry : angle 0.55214 (14980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 767 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.6557 (m-80) outliers start: 4 outliers final: 3 residues processed: 148 average time/residue: 0.1670 time to fit residues: 39.0320 Evaluate side-chains 143 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 767 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 10.0000 chunk 95 optimal weight: 0.0970 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 286 ASN B 594 HIS ** B 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.138921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.101833 restraints weight = 19552.826| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.72 r_work: 0.3350 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11000 Z= 0.169 Angle : 0.741 13.111 15028 Z= 0.348 Chirality : 0.048 0.504 1752 Planarity : 0.004 0.054 1802 Dihedral : 12.843 113.261 2162 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.53 % Favored : 93.31 % Rotamer: Outliers : 3.45 % Allowed : 27.39 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.52 (0.25), residues: 1256 helix: 1.93 (0.21), residues: 578 sheet: 0.54 (0.32), residues: 280 loop : -2.33 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 446 HIS 0.010 0.001 HIS B 636 PHE 0.021 0.002 PHE A 702 TYR 0.048 0.002 TYR A 717 ARG 0.004 0.001 ARG B 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00985 ( 8) link_NAG-ASN : angle 6.97707 ( 24) link_BETA1-4 : bond 0.00425 ( 4) link_BETA1-4 : angle 2.67055 ( 12) hydrogen bonds : bond 0.04733 ( 615) hydrogen bonds : angle 4.57489 ( 1758) metal coordination : bond 0.00322 ( 6) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.91573 ( 12) covalent geometry : bond 0.00388 (10976) covalent geometry : angle 0.68300 (14980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5493 (mt) REVERT: A 605 TYR cc_start: 0.8581 (m-80) cc_final: 0.8381 (m-80) REVERT: A 713 ASP cc_start: 0.7944 (t0) cc_final: 0.7622 (t0) REVERT: B 36 ARG cc_start: 0.4876 (OUTLIER) cc_final: 0.3170 (mtt180) REVERT: B 208 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.5501 (ppp) REVERT: B 613 MET cc_start: 0.8632 (mmm) cc_final: 0.8404 (mmm) REVERT: B 722 PHE cc_start: 0.8665 (m-10) cc_final: 0.8445 (m-10) REVERT: B 736 MET cc_start: 0.8131 (mmt) cc_final: 0.7902 (mmt) REVERT: B 767 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7825 (m-80) outliers start: 39 outliers final: 17 residues processed: 176 average time/residue: 0.1907 time to fit residues: 52.0083 Evaluate side-chains 157 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.139178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.101301 restraints weight = 19871.425| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.74 r_work: 0.3342 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 11000 Z= 0.156 Angle : 0.702 13.426 15028 Z= 0.328 Chirality : 0.048 0.499 1752 Planarity : 0.004 0.046 1802 Dihedral : 12.252 113.207 2158 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.79 % Rotamer: Outliers : 4.95 % Allowed : 27.12 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.46 (0.24), residues: 1256 helix: 1.80 (0.21), residues: 578 sheet: 0.61 (0.32), residues: 280 loop : -2.28 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 446 HIS 0.008 0.001 HIS B 636 PHE 0.024 0.001 PHE A 445 TYR 0.050 0.002 TYR A 717 ARG 0.003 0.000 ARG B 172 Details of bonding type rmsd link_NAG-ASN : bond 0.01004 ( 8) link_NAG-ASN : angle 6.89331 ( 24) link_BETA1-4 : bond 0.00511 ( 4) link_BETA1-4 : angle 2.89254 ( 12) hydrogen bonds : bond 0.04549 ( 615) hydrogen bonds : angle 4.49741 ( 1758) metal coordination : bond 0.00267 ( 6) SS BOND : bond 0.00205 ( 6) SS BOND : angle 0.79862 ( 12) covalent geometry : bond 0.00361 (10976) covalent geometry : angle 0.64073 (14980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 149 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5330 (mt) REVERT: A 605 TYR cc_start: 0.8584 (m-80) cc_final: 0.8381 (m-80) REVERT: A 702 PHE cc_start: 0.8149 (m-80) cc_final: 0.7413 (m-80) REVERT: A 713 ASP cc_start: 0.7995 (t0) cc_final: 0.7781 (t0) REVERT: B 160 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7672 (mttp) REVERT: B 208 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5511 (ppp) REVERT: B 613 MET cc_start: 0.8602 (mmm) cc_final: 0.8365 (mmm) REVERT: B 722 PHE cc_start: 0.8675 (m-10) cc_final: 0.8421 (m-10) REVERT: B 736 MET cc_start: 0.8109 (mmt) cc_final: 0.7851 (mmt) REVERT: B 767 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7782 (m-80) outliers start: 56 outliers final: 29 residues processed: 191 average time/residue: 0.2063 time to fit residues: 61.3347 Evaluate side-chains 168 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.135459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.098178 restraints weight = 19985.222| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.65 r_work: 0.3298 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11000 Z= 0.288 Angle : 0.820 14.765 15028 Z= 0.392 Chirality : 0.052 0.542 1752 Planarity : 0.005 0.046 1802 Dihedral : 12.107 115.402 2158 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.56 % Favored : 92.28 % Rotamer: Outliers : 6.01 % Allowed : 26.86 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.07 (0.24), residues: 1256 helix: 1.49 (0.21), residues: 564 sheet: 0.29 (0.31), residues: 282 loop : -2.25 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 446 HIS 0.007 0.001 HIS A 50 PHE 0.025 0.002 PHE A 808 TYR 0.033 0.002 TYR A 717 ARG 0.006 0.001 ARG A 524 Details of bonding type rmsd link_NAG-ASN : bond 0.01088 ( 8) link_NAG-ASN : angle 7.17689 ( 24) link_BETA1-4 : bond 0.00492 ( 4) link_BETA1-4 : angle 2.84219 ( 12) hydrogen bonds : bond 0.05556 ( 615) hydrogen bonds : angle 4.86154 ( 1758) metal coordination : bond 0.00529 ( 6) SS BOND : bond 0.00314 ( 6) SS BOND : angle 1.15440 ( 12) covalent geometry : bond 0.00672 (10976) covalent geometry : angle 0.76443 (14980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 144 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: A 326 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5251 (mm) REVERT: A 455 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: A 702 PHE cc_start: 0.8229 (m-80) cc_final: 0.7484 (m-80) REVERT: A 713 ASP cc_start: 0.8127 (t0) cc_final: 0.7907 (t0) REVERT: B 36 ARG cc_start: 0.5103 (OUTLIER) cc_final: 0.3430 (mtt-85) REVERT: B 160 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7766 (mttp) REVERT: B 208 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.5824 (ppp) REVERT: B 454 PHE cc_start: 0.8544 (m-80) cc_final: 0.7971 (m-80) REVERT: B 613 MET cc_start: 0.8559 (mmm) cc_final: 0.8306 (mmm) REVERT: B 722 PHE cc_start: 0.8806 (m-10) cc_final: 0.8511 (m-10) REVERT: B 767 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7937 (m-80) outliers start: 68 outliers final: 37 residues processed: 192 average time/residue: 0.1738 time to fit residues: 53.0392 Evaluate side-chains 180 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.138925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.101937 restraints weight = 19619.327| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.71 r_work: 0.3350 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11000 Z= 0.141 Angle : 0.720 14.114 15028 Z= 0.332 Chirality : 0.048 0.520 1752 Planarity : 0.004 0.038 1802 Dihedral : 11.569 113.973 2158 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 3.71 % Allowed : 29.68 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.29 (0.24), residues: 1256 helix: 1.81 (0.22), residues: 552 sheet: 0.55 (0.32), residues: 280 loop : -2.37 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 446 HIS 0.006 0.001 HIS B 636 PHE 0.023 0.001 PHE B 705 TYR 0.030 0.001 TYR A 717 ARG 0.006 0.000 ARG A 36 Details of bonding type rmsd link_NAG-ASN : bond 0.01093 ( 8) link_NAG-ASN : angle 6.95658 ( 24) link_BETA1-4 : bond 0.00342 ( 4) link_BETA1-4 : angle 3.16163 ( 12) hydrogen bonds : bond 0.04612 ( 615) hydrogen bonds : angle 4.53272 ( 1758) metal coordination : bond 0.00197 ( 6) SS BOND : bond 0.00223 ( 6) SS BOND : angle 0.82645 ( 12) covalent geometry : bond 0.00312 (10976) covalent geometry : angle 0.65924 (14980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: A 326 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5280 (mm) REVERT: A 455 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: A 702 PHE cc_start: 0.8054 (m-80) cc_final: 0.7537 (m-80) REVERT: A 713 ASP cc_start: 0.8051 (t0) cc_final: 0.7800 (t0) REVERT: B 36 ARG cc_start: 0.4993 (OUTLIER) cc_final: 0.3494 (mtt-85) REVERT: B 160 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7788 (mttp) REVERT: B 208 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.5597 (ppp) REVERT: B 454 PHE cc_start: 0.8426 (m-80) cc_final: 0.7908 (m-80) REVERT: B 613 MET cc_start: 0.8642 (mmm) cc_final: 0.8363 (mmm) REVERT: B 722 PHE cc_start: 0.8758 (m-10) cc_final: 0.8438 (m-10) REVERT: B 736 MET cc_start: 0.8086 (mmt) cc_final: 0.7860 (mmt) REVERT: B 767 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7972 (m-80) outliers start: 42 outliers final: 24 residues processed: 179 average time/residue: 0.2010 time to fit residues: 56.1191 Evaluate side-chains 170 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 482 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.139589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.102003 restraints weight = 19971.311| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.05 r_work: 0.3429 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11000 Z= 0.215 Angle : 0.765 14.515 15028 Z= 0.358 Chirality : 0.050 0.540 1752 Planarity : 0.004 0.044 1802 Dihedral : 11.400 114.292 2158 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.53 % Favored : 93.31 % Rotamer: Outliers : 4.59 % Allowed : 28.89 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.21 (0.24), residues: 1256 helix: 1.74 (0.22), residues: 552 sheet: 0.65 (0.33), residues: 268 loop : -2.44 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 446 HIS 0.005 0.001 HIS B 636 PHE 0.023 0.002 PHE B 571 TYR 0.036 0.002 TYR A 717 ARG 0.003 0.000 ARG A 524 Details of bonding type rmsd link_NAG-ASN : bond 0.01108 ( 8) link_NAG-ASN : angle 7.09654 ( 24) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 3.10969 ( 12) hydrogen bonds : bond 0.04953 ( 615) hydrogen bonds : angle 4.64406 ( 1758) metal coordination : bond 0.00397 ( 6) SS BOND : bond 0.00282 ( 6) SS BOND : angle 0.97338 ( 12) covalent geometry : bond 0.00501 (10976) covalent geometry : angle 0.70545 (14980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 143 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: A 455 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7515 (m-80) REVERT: A 702 PHE cc_start: 0.7881 (m-80) cc_final: 0.7438 (m-80) REVERT: A 713 ASP cc_start: 0.8065 (t0) cc_final: 0.7812 (t0) REVERT: A 758 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7672 (mmm) REVERT: B 36 ARG cc_start: 0.5062 (OUTLIER) cc_final: 0.3545 (mtt-85) REVERT: B 160 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7821 (mttp) REVERT: B 208 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.5560 (ppp) REVERT: B 210 TYR cc_start: 0.7208 (t80) cc_final: 0.6797 (t80) REVERT: B 454 PHE cc_start: 0.8454 (m-80) cc_final: 0.7835 (m-80) REVERT: B 613 MET cc_start: 0.8612 (mmm) cc_final: 0.8331 (mmm) REVERT: B 722 PHE cc_start: 0.8771 (m-10) cc_final: 0.8471 (m-10) REVERT: B 736 MET cc_start: 0.8126 (mmt) cc_final: 0.7890 (mmt) REVERT: B 767 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7918 (m-80) outliers start: 52 outliers final: 36 residues processed: 183 average time/residue: 0.1878 time to fit residues: 53.8189 Evaluate side-chains 181 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 767 PHE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 0.1980 chunk 100 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 96 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 796 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.143107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.105211 restraints weight = 19949.525| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.11 r_work: 0.3476 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.848 11000 Z= 0.297 Angle : 0.708 13.962 15028 Z= 0.323 Chirality : 0.047 0.509 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.966 112.679 2158 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.78 % Favored : 95.06 % Rotamer: Outliers : 3.18 % Allowed : 30.39 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.41 (0.24), residues: 1256 helix: 1.90 (0.22), residues: 552 sheet: 0.82 (0.34), residues: 268 loop : -2.37 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 446 HIS 0.004 0.001 HIS B 636 PHE 0.026 0.001 PHE B 705 TYR 0.017 0.001 TYR A 709 ARG 0.003 0.000 ARG B 79 Details of bonding type rmsd link_NAG-ASN : bond 0.01081 ( 8) link_NAG-ASN : angle 6.85241 ( 24) link_BETA1-4 : bond 0.00286 ( 4) link_BETA1-4 : angle 3.35081 ( 12) hydrogen bonds : bond 0.04231 ( 615) hydrogen bonds : angle 4.42664 ( 1758) metal coordination : bond 0.34618 ( 6) SS BOND : bond 0.00195 ( 6) SS BOND : angle 0.73685 ( 12) covalent geometry : bond 0.00267 (10976) covalent geometry : angle 0.64697 (14980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: A 455 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: A 617 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8806 (pp) REVERT: A 702 PHE cc_start: 0.7978 (m-80) cc_final: 0.7527 (m-80) REVERT: A 713 ASP cc_start: 0.8063 (t0) cc_final: 0.7783 (t0) REVERT: B 36 ARG cc_start: 0.4892 (OUTLIER) cc_final: 0.3483 (mtt-85) REVERT: B 160 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7888 (mttp) REVERT: B 208 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.5249 (ppp) REVERT: B 613 MET cc_start: 0.8642 (mmm) cc_final: 0.8268 (mmm) REVERT: B 722 PHE cc_start: 0.8753 (m-10) cc_final: 0.8420 (m-10) REVERT: B 736 MET cc_start: 0.8143 (mmt) cc_final: 0.7827 (mmt) REVERT: B 767 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7883 (m-80) outliers start: 36 outliers final: 20 residues processed: 175 average time/residue: 0.1851 time to fit residues: 51.9897 Evaluate side-chains 163 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.142932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.105113 restraints weight = 19633.962| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.09 r_work: 0.3481 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11000 Z= 0.137 Angle : 0.723 14.042 15028 Z= 0.331 Chirality : 0.047 0.515 1752 Planarity : 0.004 0.039 1802 Dihedral : 10.744 112.745 2156 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 3.71 % Allowed : 29.95 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.45 (0.24), residues: 1256 helix: 1.91 (0.22), residues: 552 sheet: 0.89 (0.34), residues: 268 loop : -2.36 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 446 HIS 0.004 0.001 HIS B 800 PHE 0.029 0.001 PHE A 705 TYR 0.043 0.001 TYR A 717 ARG 0.006 0.000 ARG B 518 Details of bonding type rmsd link_NAG-ASN : bond 0.01081 ( 8) link_NAG-ASN : angle 6.88566 ( 24) link_BETA1-4 : bond 0.00307 ( 4) link_BETA1-4 : angle 3.35166 ( 12) hydrogen bonds : bond 0.04252 ( 615) hydrogen bonds : angle 4.39525 ( 1758) metal coordination : bond 0.00479 ( 6) SS BOND : bond 0.00253 ( 6) SS BOND : angle 0.97602 ( 12) covalent geometry : bond 0.00308 (10976) covalent geometry : angle 0.66280 (14980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: A 326 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5178 (mt) REVERT: A 455 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: A 702 PHE cc_start: 0.7848 (m-80) cc_final: 0.7422 (m-80) REVERT: A 713 ASP cc_start: 0.8043 (t0) cc_final: 0.7805 (m-30) REVERT: B 36 ARG cc_start: 0.4920 (OUTLIER) cc_final: 0.3493 (mtt-85) REVERT: B 208 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.5300 (ppp) REVERT: B 613 MET cc_start: 0.8530 (mmm) cc_final: 0.8225 (mmm) REVERT: B 722 PHE cc_start: 0.8722 (m-10) cc_final: 0.8399 (m-10) REVERT: B 736 MET cc_start: 0.8152 (mmt) cc_final: 0.7863 (mmt) REVERT: B 767 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7833 (m-80) outliers start: 42 outliers final: 31 residues processed: 177 average time/residue: 0.2037 time to fit residues: 56.9053 Evaluate side-chains 178 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 7 optimal weight: 0.3980 chunk 106 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.142764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.104843 restraints weight = 19881.255| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.09 r_work: 0.3487 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11000 Z= 0.127 Angle : 0.717 13.957 15028 Z= 0.325 Chirality : 0.047 0.511 1752 Planarity : 0.004 0.038 1802 Dihedral : 10.549 112.278 2156 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 3.27 % Allowed : 30.12 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.51 (0.24), residues: 1256 helix: 1.96 (0.22), residues: 554 sheet: 0.95 (0.34), residues: 268 loop : -2.37 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 446 HIS 0.004 0.001 HIS B 636 PHE 0.031 0.001 PHE A 705 TYR 0.031 0.001 TYR A 481 ARG 0.003 0.000 ARG B 518 Details of bonding type rmsd link_NAG-ASN : bond 0.01088 ( 8) link_NAG-ASN : angle 6.83441 ( 24) link_BETA1-4 : bond 0.00304 ( 4) link_BETA1-4 : angle 3.44340 ( 12) hydrogen bonds : bond 0.04095 ( 615) hydrogen bonds : angle 4.34027 ( 1758) metal coordination : bond 0.00484 ( 6) SS BOND : bond 0.00212 ( 6) SS BOND : angle 0.94206 ( 12) covalent geometry : bond 0.00278 (10976) covalent geometry : angle 0.65671 (14980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: A 326 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5210 (mt) REVERT: A 455 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: A 689 MET cc_start: 0.8869 (mmt) cc_final: 0.8621 (mmp) REVERT: A 702 PHE cc_start: 0.7823 (m-80) cc_final: 0.7416 (m-80) REVERT: A 713 ASP cc_start: 0.7985 (t0) cc_final: 0.7734 (m-30) REVERT: B 36 ARG cc_start: 0.4917 (OUTLIER) cc_final: 0.3502 (mtt-85) REVERT: B 208 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.5313 (ppp) REVERT: B 221 MET cc_start: 0.7842 (mmm) cc_final: 0.7544 (mmm) REVERT: B 613 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8206 (mmm) REVERT: B 722 PHE cc_start: 0.8753 (m-10) cc_final: 0.8440 (m-10) REVERT: B 736 MET cc_start: 0.8140 (mmt) cc_final: 0.7802 (mmt) REVERT: B 767 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7858 (m-80) outliers start: 37 outliers final: 29 residues processed: 174 average time/residue: 0.1978 time to fit residues: 54.3147 Evaluate side-chains 177 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.140195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.102392 restraints weight = 20124.828| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.10 r_work: 0.3432 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11000 Z= 0.222 Angle : 0.783 14.573 15028 Z= 0.365 Chirality : 0.050 0.542 1752 Planarity : 0.004 0.041 1802 Dihedral : 10.709 113.910 2156 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.13 % Favored : 93.71 % Rotamer: Outliers : 4.06 % Allowed : 30.12 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.33 (0.24), residues: 1256 helix: 1.80 (0.22), residues: 550 sheet: 0.74 (0.33), residues: 268 loop : -2.32 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 446 HIS 0.005 0.001 HIS B 636 PHE 0.041 0.002 PHE A 705 TYR 0.030 0.002 TYR A 481 ARG 0.004 0.000 ARG B 518 Details of bonding type rmsd link_NAG-ASN : bond 0.01118 ( 8) link_NAG-ASN : angle 7.07552 ( 24) link_BETA1-4 : bond 0.00286 ( 4) link_BETA1-4 : angle 3.40624 ( 12) hydrogen bonds : bond 0.04808 ( 615) hydrogen bonds : angle 4.53916 ( 1758) metal coordination : bond 0.00810 ( 6) SS BOND : bond 0.00246 ( 6) SS BOND : angle 1.07841 ( 12) covalent geometry : bond 0.00515 (10976) covalent geometry : angle 0.72464 (14980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: A 455 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: A 689 MET cc_start: 0.8910 (mmt) cc_final: 0.8661 (mmp) REVERT: A 702 PHE cc_start: 0.7924 (m-80) cc_final: 0.7459 (m-80) REVERT: A 713 ASP cc_start: 0.8072 (t0) cc_final: 0.7795 (t0) REVERT: B 36 ARG cc_start: 0.4973 (OUTLIER) cc_final: 0.3444 (mtt-85) REVERT: B 208 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.5463 (ppp) REVERT: B 536 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.6501 (t80) REVERT: B 613 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8216 (mmm) REVERT: B 722 PHE cc_start: 0.8789 (m-10) cc_final: 0.8532 (m-10) REVERT: B 736 MET cc_start: 0.8159 (mmt) cc_final: 0.7856 (mmt) REVERT: B 767 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7923 (m-80) outliers start: 46 outliers final: 33 residues processed: 179 average time/residue: 0.2399 time to fit residues: 68.6189 Evaluate side-chains 178 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.141596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.103693 restraints weight = 19787.319| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.09 r_work: 0.3470 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11000 Z= 0.140 Angle : 0.736 14.162 15028 Z= 0.335 Chirality : 0.047 0.522 1752 Planarity : 0.004 0.040 1802 Dihedral : 10.502 113.073 2156 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 3.53 % Allowed : 30.57 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.44 (0.24), residues: 1256 helix: 1.91 (0.22), residues: 552 sheet: 0.82 (0.33), residues: 268 loop : -2.33 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 446 HIS 0.004 0.001 HIS B 636 PHE 0.042 0.002 PHE A 705 TYR 0.030 0.001 TYR A 481 ARG 0.003 0.000 ARG B 79 Details of bonding type rmsd link_NAG-ASN : bond 0.01064 ( 8) link_NAG-ASN : angle 6.92621 ( 24) link_BETA1-4 : bond 0.00244 ( 4) link_BETA1-4 : angle 3.50661 ( 12) hydrogen bonds : bond 0.04359 ( 615) hydrogen bonds : angle 4.39867 ( 1758) metal coordination : bond 0.00409 ( 6) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.93239 ( 12) covalent geometry : bond 0.00313 (10976) covalent geometry : angle 0.67479 (14980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5591.10 seconds wall clock time: 102 minutes 59.58 seconds (6179.58 seconds total)