Starting phenix.real_space_refine on Tue May 13 17:04:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wos_37697/05_2025/8wos_37697_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wos_37697/05_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_37697/05_2025/8wos_37697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wos_37697/05_2025/8wos_37697.map" model { file = "/net/cci-nas-00/data/ceres_data/8wos_37697/05_2025/8wos_37697_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wos_37697/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.22, per 1000 atoms: 0.68 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: 2.78 Conformation dependent library (CDL) restraints added in 1.3 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: 1.00 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: 3.44 Time building geometry restraints manager: 3.26 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: 0.07 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: 2.200 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.760 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.180 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- 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 : 1.096 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: 0.1784 time to fit residues: 41.7455 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 : 1.081 ------------------------------------------------------------------------------- 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 = 0.138920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.101831 restraints weight = 19553.147| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.71 r_work: 0.3353 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 13.110 15028 Z= 0.348 Chirality : 0.048 0.504 1752 Planarity : 0.004 0.054 1802 Dihedral : 12.845 113.263 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 : 3.53 % Allowed : 27.30 % 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: 0.51 (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 6.97708 ( 24) link_BETA1-4 : bond 0.00427 ( 4) link_BETA1-4 : angle 2.67031 ( 12) hydrogen bonds : bond 0.04733 ( 615) hydrogen bonds : angle 4.57500 ( 1758) metal coordination : bond 0.00322 ( 6) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.91648 ( 12) covalent geometry : bond 0.00388 (10976) covalent geometry : angle 0.68305 (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 188 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5485 (mt) REVERT: A 605 TYR cc_start: 0.8573 (m-80) cc_final: 0.8373 (m-80) REVERT: A 713 ASP cc_start: 0.7928 (t0) cc_final: 0.7608 (t0) REVERT: B 36 ARG cc_start: 0.4875 (OUTLIER) cc_final: 0.3177 (mtt180) REVERT: B 208 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.5511 (ppp) REVERT: B 613 MET cc_start: 0.8629 (mmm) cc_final: 0.8401 (mmm) REVERT: B 722 PHE cc_start: 0.8664 (m-10) cc_final: 0.8446 (m-10) REVERT: B 736 MET cc_start: 0.8128 (mmt) cc_final: 0.7897 (mmt) REVERT: B 767 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7825 (m-80) outliers start: 40 outliers final: 17 residues processed: 177 average time/residue: 0.1806 time to fit residues: 49.1624 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 : 1.198 ------------------------------------------------------------------------------- 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: 3.9990 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 107 optimal weight: 0.0270 overall best weight: 0.7842 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.139891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.102434 restraints weight = 19793.334| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.63 r_work: 0.3360 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 11000 Z= 0.136 Angle : 0.699 13.161 15028 Z= 0.323 Chirality : 0.047 0.495 1752 Planarity : 0.004 0.046 1802 Dihedral : 12.324 112.589 2158 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 3.80 % Allowed : 27.21 % Favored : 68.99 % 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: 1.85 (0.21), residues: 578 sheet: 0.66 (0.32), residues: 280 loop : -2.28 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 446 HIS 0.007 0.001 HIS B 636 PHE 0.023 0.001 PHE A 445 TYR 0.046 0.001 TYR A 717 ARG 0.003 0.000 ARG B 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00994 ( 8) link_NAG-ASN : angle 6.88575 ( 24) link_BETA1-4 : bond 0.00488 ( 4) link_BETA1-4 : angle 2.92907 ( 12) hydrogen bonds : bond 0.04384 ( 615) hydrogen bonds : angle 4.47037 ( 1758) metal coordination : bond 0.00198 ( 6) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.71314 ( 12) covalent geometry : bond 0.00313 (10976) covalent geometry : angle 0.63762 (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 195 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 326 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5526 (mt) REVERT: A 605 TYR cc_start: 0.8572 (m-80) cc_final: 0.8365 (m-80) REVERT: A 713 ASP cc_start: 0.8043 (t0) cc_final: 0.7803 (t0) REVERT: B 160 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7663 (mttp) REVERT: B 208 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.5432 (ppp) REVERT: B 613 MET cc_start: 0.8621 (mmm) cc_final: 0.8382 (mmm) REVERT: B 722 PHE cc_start: 0.8673 (m-10) cc_final: 0.8426 (m-10) REVERT: B 736 MET cc_start: 0.8139 (mmt) cc_final: 0.7882 (mmt) REVERT: B 767 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7734 (m-80) outliers start: 43 outliers final: 19 residues processed: 186 average time/residue: 0.1672 time to fit residues: 48.3856 Evaluate side-chains 160 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 536 TYR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.137390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098440 restraints weight = 19793.715| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.14 r_work: 0.3350 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11000 Z= 0.217 Angle : 0.755 14.200 15028 Z= 0.355 Chirality : 0.049 0.512 1752 Planarity : 0.004 0.045 1802 Dihedral : 11.940 114.267 2156 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.93 % Favored : 92.91 % Rotamer: Outliers : 5.65 % Allowed : 27.03 % Favored : 67.31 % 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: 0.26 (0.24), residues: 1256 helix: 1.72 (0.22), residues: 564 sheet: 0.73 (0.33), residues: 268 loop : -2.48 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 446 HIS 0.006 0.001 HIS B 636 PHE 0.022 0.002 PHE B 705 TYR 0.056 0.002 TYR A 717 ARG 0.007 0.001 ARG A 524 Details of bonding type rmsd link_NAG-ASN : bond 0.01046 ( 8) link_NAG-ASN : angle 7.00613 ( 24) link_BETA1-4 : bond 0.00527 ( 4) link_BETA1-4 : angle 2.84886 ( 12) hydrogen bonds : bond 0.04964 ( 615) hydrogen bonds : angle 4.62600 ( 1758) metal coordination : bond 0.00396 ( 6) SS BOND : bond 0.00252 ( 6) SS BOND : angle 0.93007 ( 12) covalent geometry : bond 0.00506 (10976) covalent geometry : angle 0.69694 (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 213 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 149 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7786 (tp) cc_final: 0.7331 (mp) REVERT: A 294 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: A 326 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5213 (mt) REVERT: A 455 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: A 702 PHE cc_start: 0.8101 (m-80) cc_final: 0.7324 (m-80) REVERT: A 713 ASP cc_start: 0.8107 (t0) cc_final: 0.7744 (t0) REVERT: B 36 ARG cc_start: 0.4961 (OUTLIER) cc_final: 0.3320 (mtt180) REVERT: B 160 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7631 (mttp) REVERT: B 208 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.5564 (ppp) REVERT: B 454 PHE cc_start: 0.8512 (m-80) cc_final: 0.7849 (m-80) REVERT: B 613 MET cc_start: 0.8532 (mmm) cc_final: 0.8287 (mmm) REVERT: B 722 PHE cc_start: 0.8757 (m-10) cc_final: 0.8476 (m-10) REVERT: B 767 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7774 (m-80) outliers start: 64 outliers final: 36 residues processed: 195 average time/residue: 0.1665 time to fit residues: 50.4235 Evaluate side-chains 182 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG 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 326 LEU Chi-restraints excluded: chain A residue 443 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 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 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 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 484 LEU 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 799 TRP 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: 0.9990 chunk 91 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 0.0470 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.0370 chunk 45 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.140439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.103304 restraints weight = 19500.965| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.69 r_work: 0.3373 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11000 Z= 0.124 Angle : 0.697 13.697 15028 Z= 0.319 Chirality : 0.047 0.503 1752 Planarity : 0.004 0.045 1802 Dihedral : 11.440 113.034 2156 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.94 % Favored : 94.90 % Rotamer: Outliers : 2.92 % Allowed : 29.42 % Favored : 67.67 % 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: 0.47 (0.24), residues: 1256 helix: 1.88 (0.22), residues: 564 sheet: 0.94 (0.34), residues: 268 loop : -2.43 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 446 HIS 0.005 0.001 HIS B 636 PHE 0.024 0.001 PHE A 445 TYR 0.056 0.001 TYR A 717 ARG 0.003 0.000 ARG A 524 Details of bonding type rmsd link_NAG-ASN : bond 0.01070 ( 8) link_NAG-ASN : angle 6.84671 ( 24) link_BETA1-4 : bond 0.00425 ( 4) link_BETA1-4 : angle 3.16025 ( 12) hydrogen bonds : bond 0.04278 ( 615) hydrogen bonds : angle 4.40975 ( 1758) metal coordination : bond 0.00143 ( 6) SS BOND : bond 0.00192 ( 6) SS BOND : angle 0.73964 ( 12) covalent geometry : bond 0.00266 (10976) covalent geometry : angle 0.63503 (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 180 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7814 (tp) cc_final: 0.7388 (mp) REVERT: A 702 PHE cc_start: 0.7942 (m-80) cc_final: 0.7453 (m-80) REVERT: A 713 ASP cc_start: 0.8072 (t0) cc_final: 0.7797 (t0) REVERT: B 36 ARG cc_start: 0.4896 (OUTLIER) cc_final: 0.3406 (mtt-85) REVERT: B 160 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7735 (mttp) REVERT: B 208 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.5429 (ppp) REVERT: B 613 MET cc_start: 0.8644 (mmm) cc_final: 0.8372 (mmm) REVERT: B 722 PHE cc_start: 0.8739 (m-10) cc_final: 0.8435 (m-10) REVERT: B 736 MET cc_start: 0.8101 (mmt) cc_final: 0.7867 (mmt) REVERT: B 767 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7675 (m-80) outliers start: 33 outliers final: 20 residues processed: 169 average time/residue: 0.1736 time to fit residues: 45.2169 Evaluate side-chains 161 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 443 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 686 MET 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 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 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: 4.9990 chunk 92 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 chunk 29 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 85 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN 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 = 0.4038 r_free = 0.4038 target = 0.137626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.100365 restraints weight = 19845.932| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.71 r_work: 0.3333 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11000 Z= 0.204 Angle : 0.744 14.380 15028 Z= 0.348 Chirality : 0.049 0.526 1752 Planarity : 0.004 0.045 1802 Dihedral : 11.214 113.837 2156 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.13 % Favored : 93.71 % Rotamer: Outliers : 4.59 % Allowed : 28.62 % Favored : 66.78 % 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: 0.37 (0.24), residues: 1256 helix: 1.86 (0.22), residues: 554 sheet: 0.82 (0.34), residues: 268 loop : -2.42 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 446 HIS 0.005 0.001 HIS A 50 PHE 0.024 0.002 PHE B 705 TYR 0.049 0.002 TYR A 717 ARG 0.005 0.000 ARG B 518 Details of bonding type rmsd link_NAG-ASN : bond 0.01084 ( 8) link_NAG-ASN : angle 7.02739 ( 24) link_BETA1-4 : bond 0.00377 ( 4) link_BETA1-4 : angle 3.08241 ( 12) hydrogen bonds : bond 0.04758 ( 615) hydrogen bonds : angle 4.54537 ( 1758) metal coordination : bond 0.00404 ( 6) SS BOND : bond 0.00280 ( 6) SS BOND : angle 0.95993 ( 12) covalent geometry : bond 0.00476 (10976) covalent geometry : angle 0.68446 (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 200 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7905 (tp) cc_final: 0.7476 (mp) REVERT: A 294 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: A 326 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5216 (mt) REVERT: A 455 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: A 702 PHE cc_start: 0.8088 (m-80) cc_final: 0.7600 (m-80) REVERT: A 713 ASP cc_start: 0.8143 (t0) cc_final: 0.7883 (t0) REVERT: B 36 ARG cc_start: 0.5013 (OUTLIER) cc_final: 0.3480 (mtt-85) REVERT: B 160 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7783 (mttp) REVERT: B 208 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.5605 (ppp) REVERT: B 454 PHE cc_start: 0.8466 (m-80) cc_final: 0.7773 (m-80) REVERT: B 613 MET cc_start: 0.8657 (mmm) cc_final: 0.8393 (mmm) REVERT: B 722 PHE cc_start: 0.8802 (m-10) cc_final: 0.8493 (m-10) REVERT: B 736 MET cc_start: 0.8118 (mmt) cc_final: 0.7870 (mmt) REVERT: B 767 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7878 (m-80) outliers start: 52 outliers final: 35 residues processed: 185 average time/residue: 0.1680 time to fit residues: 48.3707 Evaluate side-chains 185 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 326 LEU Chi-restraints excluded: chain A residue 443 ILE 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 686 MET 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 757 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 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 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 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.140491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.101142 restraints weight = 19805.452| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.18 r_work: 0.3396 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11000 Z= 0.126 Angle : 0.705 13.917 15028 Z= 0.322 Chirality : 0.047 0.512 1752 Planarity : 0.004 0.059 1802 Dihedral : 10.890 112.750 2156 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.94 % Favored : 94.90 % Rotamer: Outliers : 3.18 % Allowed : 29.51 % Favored : 67.31 % 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: 1.84 (0.22), residues: 564 sheet: 0.99 (0.34), residues: 268 loop : -2.48 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 446 HIS 0.005 0.001 HIS B 636 PHE 0.026 0.001 PHE B 705 TYR 0.053 0.001 TYR A 717 ARG 0.006 0.000 ARG A 36 Details of bonding type rmsd link_NAG-ASN : bond 0.01115 ( 8) link_NAG-ASN : angle 6.84446 ( 24) link_BETA1-4 : bond 0.00349 ( 4) link_BETA1-4 : angle 3.31389 ( 12) hydrogen bonds : bond 0.04238 ( 615) hydrogen bonds : angle 4.39818 ( 1758) metal coordination : bond 0.00110 ( 6) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.84555 ( 12) covalent geometry : bond 0.00274 (10976) covalent geometry : angle 0.64336 (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 182 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7798 (tp) cc_final: 0.7357 (mp) REVERT: A 326 LEU cc_start: 0.5914 (OUTLIER) cc_final: 0.5370 (mt) REVERT: A 702 PHE cc_start: 0.7944 (m-80) cc_final: 0.7538 (m-80) REVERT: A 713 ASP cc_start: 0.8056 (t0) cc_final: 0.7754 (t0) REVERT: B 36 ARG cc_start: 0.4888 (OUTLIER) cc_final: 0.3512 (mtt-85) REVERT: B 160 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7773 (mttp) REVERT: B 208 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.5321 (ppp) REVERT: B 613 MET cc_start: 0.8683 (mmm) cc_final: 0.8308 (mmm) REVERT: B 722 PHE cc_start: 0.8778 (m-10) cc_final: 0.8441 (m-10) REVERT: B 736 MET cc_start: 0.8107 (mmt) cc_final: 0.7844 (mmt) REVERT: B 767 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7746 (m-80) outliers start: 36 outliers final: 25 residues processed: 172 average time/residue: 0.1735 time to fit residues: 46.5753 Evaluate side-chains 175 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 451 ILE 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 686 MET Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 776 THR 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 443 ILE Chi-restraints excluded: chain B residue 453 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 116 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 56 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.143719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.106173 restraints weight = 19539.261| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.04 r_work: 0.3520 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11000 Z= 0.118 Angle : 0.702 13.742 15028 Z= 0.318 Chirality : 0.046 0.508 1752 Planarity : 0.004 0.036 1802 Dihedral : 10.495 111.757 2156 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.10 % Favored : 94.75 % Rotamer: Outliers : 2.92 % Allowed : 30.30 % Favored : 66.78 % 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: 0.53 (0.24), residues: 1256 helix: 1.90 (0.22), residues: 566 sheet: 1.10 (0.33), residues: 268 loop : -2.48 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 446 HIS 0.004 0.001 HIS B 636 PHE 0.027 0.001 PHE B 705 TYR 0.049 0.001 TYR A 717 ARG 0.003 0.000 ARG B 79 Details of bonding type rmsd link_NAG-ASN : bond 0.01085 ( 8) link_NAG-ASN : angle 6.76851 ( 24) link_BETA1-4 : bond 0.00284 ( 4) link_BETA1-4 : angle 3.40644 ( 12) hydrogen bonds : bond 0.03953 ( 615) hydrogen bonds : angle 4.32594 ( 1758) metal coordination : bond 0.00109 ( 6) SS BOND : bond 0.00189 ( 6) SS BOND : angle 0.72115 ( 12) covalent geometry : bond 0.00253 (10976) covalent geometry : angle 0.64121 (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 186 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7801 (tp) cc_final: 0.7399 (mp) REVERT: A 326 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5481 (mt) REVERT: A 702 PHE cc_start: 0.7865 (m-80) cc_final: 0.7476 (m-80) REVERT: A 713 ASP cc_start: 0.7870 (t0) cc_final: 0.7568 (m-30) REVERT: B 36 ARG cc_start: 0.4840 (OUTLIER) cc_final: 0.3647 (mtt-85) REVERT: B 613 MET cc_start: 0.8604 (mmm) cc_final: 0.8303 (mmm) REVERT: B 722 PHE cc_start: 0.8703 (m-10) cc_final: 0.8379 (m-10) REVERT: B 736 MET cc_start: 0.8172 (mmt) cc_final: 0.7833 (mmt) REVERT: B 767 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: B 799 TRP cc_start: 0.7804 (t-100) cc_final: 0.7286 (t-100) outliers start: 33 outliers final: 23 residues processed: 179 average time/residue: 0.1646 time to fit residues: 46.4485 Evaluate side-chains 171 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 686 MET 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 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 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 484 LEU 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: 10.0000 chunk 7 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 119 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B 796 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.143496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.105652 restraints weight = 19826.117| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.06 r_work: 0.3512 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.857 11000 Z= 0.299 Angle : 0.714 13.735 15028 Z= 0.322 Chirality : 0.047 0.505 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.354 111.568 2156 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.94 % Favored : 94.90 % Rotamer: Outliers : 3.36 % Allowed : 29.95 % Favored : 66.70 % 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 (0.24), residues: 1256 helix: 1.86 (0.22), residues: 566 sheet: 1.12 (0.33), residues: 268 loop : -2.46 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 446 HIS 0.003 0.001 HIS A 636 PHE 0.027 0.001 PHE A 445 TYR 0.044 0.001 TYR A 717 ARG 0.003 0.000 ARG B 79 Details of bonding type rmsd link_NAG-ASN : bond 0.01083 ( 8) link_NAG-ASN : angle 6.77452 ( 24) link_BETA1-4 : bond 0.00281 ( 4) link_BETA1-4 : angle 3.44343 ( 12) hydrogen bonds : bond 0.03986 ( 615) hydrogen bonds : angle 4.30692 ( 1758) metal coordination : bond 0.34981 ( 6) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.67902 ( 12) covalent geometry : bond 0.00275 (10976) covalent geometry : angle 0.65468 (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 185 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7817 (tp) cc_final: 0.7414 (mp) REVERT: A 326 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5326 (mt) REVERT: A 702 PHE cc_start: 0.7871 (m-80) cc_final: 0.7445 (m-80) REVERT: A 713 ASP cc_start: 0.7847 (t0) cc_final: 0.7559 (m-30) REVERT: B 36 ARG cc_start: 0.4805 (OUTLIER) cc_final: 0.3593 (mtt-85) REVERT: B 160 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7793 (mttp) REVERT: B 221 MET cc_start: 0.7866 (mmm) cc_final: 0.7474 (mmm) REVERT: B 586 MET cc_start: 0.8392 (mmm) cc_final: 0.8168 (mmm) REVERT: B 613 MET cc_start: 0.8561 (mmm) cc_final: 0.8247 (mmm) REVERT: B 722 PHE cc_start: 0.8751 (m-10) cc_final: 0.8435 (m-10) REVERT: B 767 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7663 (m-80) outliers start: 38 outliers final: 31 residues processed: 176 average time/residue: 0.1693 time to fit residues: 47.1295 Evaluate side-chains 179 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 240 MET 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 512 LEU Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 686 MET 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 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 160 LYS 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 455 TYR Chi-restraints excluded: chain B residue 484 LEU 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: 1.9990 chunk 98 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 118 optimal weight: 0.0170 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 461 GLN ** 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 = 0.4127 r_free = 0.4127 target = 0.143016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.105095 restraints weight = 19781.229| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.07 r_work: 0.3490 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2422 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= 0.133 Angle : 0.718 13.895 15028 Z= 0.326 Chirality : 0.047 0.512 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.218 111.635 2156 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.75 % Rotamer: Outliers : 3.45 % Allowed : 29.86 % Favored : 66.70 % 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: 0.49 (0.24), residues: 1256 helix: 1.83 (0.22), residues: 566 sheet: 1.08 (0.33), residues: 268 loop : -2.44 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 446 HIS 0.008 0.001 HIS B 796 PHE 0.032 0.001 PHE A 705 TYR 0.052 0.001 TYR A 717 ARG 0.003 0.000 ARG B 79 Details of bonding type rmsd link_NAG-ASN : bond 0.01083 ( 8) link_NAG-ASN : angle 6.80555 ( 24) link_BETA1-4 : bond 0.00267 ( 4) link_BETA1-4 : angle 3.45986 ( 12) hydrogen bonds : bond 0.04135 ( 615) hydrogen bonds : angle 4.30767 ( 1758) metal coordination : bond 0.00691 ( 6) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.69926 ( 12) covalent geometry : bond 0.00296 (10976) covalent geometry : angle 0.65803 (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 183 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7812 (tp) cc_final: 0.7433 (mp) REVERT: A 326 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5333 (mt) REVERT: A 689 MET cc_start: 0.9395 (mmp) cc_final: 0.9153 (mmt) REVERT: A 702 PHE cc_start: 0.7891 (m-80) cc_final: 0.7456 (m-80) REVERT: A 713 ASP cc_start: 0.7842 (t0) cc_final: 0.7595 (m-30) REVERT: B 36 ARG cc_start: 0.4734 (OUTLIER) cc_final: 0.3554 (mtt-85) REVERT: B 221 MET cc_start: 0.7876 (mmm) cc_final: 0.7521 (mmm) REVERT: B 586 MET cc_start: 0.8428 (mmm) cc_final: 0.8189 (mmm) REVERT: B 613 MET cc_start: 0.8596 (mmm) cc_final: 0.8319 (mmm) REVERT: B 722 PHE cc_start: 0.8788 (m-10) cc_final: 0.8458 (m-10) REVERT: B 767 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7707 (m-80) outliers start: 39 outliers final: 32 residues processed: 173 average time/residue: 0.1609 time to fit residues: 43.6926 Evaluate side-chains 177 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 292 ASN 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 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 686 MET 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 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 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 453 VAL Chi-restraints excluded: chain B residue 484 LEU 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: 2.9990 chunk 98 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.140675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.102699 restraints weight = 19824.589| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.05 r_work: 0.3463 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11000 Z= 0.194 Angle : 0.763 14.236 15028 Z= 0.350 Chirality : 0.048 0.528 1752 Planarity : 0.004 0.040 1802 Dihedral : 10.304 112.707 2156 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 3.27 % Allowed : 30.57 % Favored : 66.17 % 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: 0.42 (0.24), residues: 1256 helix: 1.84 (0.22), residues: 554 sheet: 0.91 (0.33), residues: 268 loop : -2.35 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 446 HIS 0.004 0.001 HIS A 50 PHE 0.034 0.002 PHE A 705 TYR 0.025 0.002 TYR A 188 ARG 0.002 0.000 ARG B 79 Details of bonding type rmsd link_NAG-ASN : bond 0.01088 ( 8) link_NAG-ASN : angle 6.99095 ( 24) link_BETA1-4 : bond 0.00279 ( 4) link_BETA1-4 : angle 3.46798 ( 12) hydrogen bonds : bond 0.04602 ( 615) hydrogen bonds : angle 4.46083 ( 1758) metal coordination : bond 0.01019 ( 6) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.86354 ( 12) covalent geometry : bond 0.00448 (10976) covalent geometry : angle 0.70348 (14980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4884.82 seconds wall clock time: 85 minutes 43.73 seconds (5143.73 seconds total)