Starting phenix.real_space_refine on Sat Aug 23 08:10:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wos_37697/08_2025/8wos_37697_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wos_37697/08_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_37697/08_2025/8wos_37697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wos_37697/08_2025/8wos_37697.map" model { file = "/net/cci-nas-00/data/ceres_data/8wos_37697/08_2025/8wos_37697_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wos_37697/08_2025/8wos_37697_neut.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.03, per 1000 atoms: 0.28 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: 1.10 Conformation dependent library (CDL) restraints added in 293.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.35 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: 1.89 Time building geometry restraints manager: 1.41 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: 0.02 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: 3.160 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.720 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- 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 : 39.36 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 785 TYR 0.032 0.001 TYR A 717 PHE 0.050 0.001 PHE A 702 TRP 0.028 0.001 TRP A 446 HIS 0.005 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00316 (10976) covalent geometry : angle 0.55214 (14980) SS BOND : bond 0.00186 ( 6) SS BOND : angle 1.09562 ( 12) hydrogen bonds : bond 0.10129 ( 615) hydrogen bonds : angle 4.85068 ( 1758) metal coordination : bond 0.00167 ( 6) link_BETA1-4 : bond 0.00198 ( 4) link_BETA1-4 : angle 1.52023 ( 12) link_NAG-ASN : bond 0.00621 ( 8) link_NAG-ASN : angle 5.10714 ( 24) *********************** 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 : 0.425 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: 0.0692 time to fit residues: 16.6871 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 : 0.396 ------------------------------------------------------------------------------- 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 108 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.8444 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.138104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.100414 restraints weight = 19856.326| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.72 r_work: 0.3329 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11000 Z= 0.195 Angle : 0.757 13.514 15028 Z= 0.358 Chirality : 0.049 0.497 1752 Planarity : 0.004 0.055 1802 Dihedral : 13.000 113.764 2162 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.61 % Favored : 93.23 % Rotamer: Outliers : 3.80 % Allowed : 27.65 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.24), residues: 1256 helix: 1.82 (0.21), residues: 578 sheet: 0.48 (0.32), residues: 280 loop : -2.36 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 79 TYR 0.046 0.002 TYR A 717 PHE 0.020 0.002 PHE A 702 TRP 0.025 0.002 TRP A 446 HIS 0.010 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00452 (10976) covalent geometry : angle 0.69894 (14980) SS BOND : bond 0.00264 ( 6) SS BOND : angle 1.01224 ( 12) hydrogen bonds : bond 0.04898 ( 615) hydrogen bonds : angle 4.64048 ( 1758) metal coordination : bond 0.00380 ( 6) link_BETA1-4 : bond 0.00405 ( 4) link_BETA1-4 : angle 2.64222 ( 12) link_NAG-ASN : bond 0.00962 ( 8) link_NAG-ASN : angle 7.04056 ( 24) *********************** 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 193 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5286 (mt) REVERT: A 605 TYR cc_start: 0.8576 (m-80) cc_final: 0.8371 (m-80) REVERT: A 713 ASP cc_start: 0.7998 (t0) cc_final: 0.7677 (t0) REVERT: B 36 ARG cc_start: 0.4954 (OUTLIER) cc_final: 0.3177 (mtt180) REVERT: B 160 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7694 (mttp) REVERT: B 208 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.5557 (ppp) REVERT: B 613 MET cc_start: 0.8622 (mmm) cc_final: 0.8399 (mmm) REVERT: B 722 PHE cc_start: 0.8725 (m-10) cc_final: 0.8501 (m-10) REVERT: B 736 MET cc_start: 0.8147 (mmt) cc_final: 0.7924 (mmt) REVERT: B 767 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7818 (m-80) outliers start: 43 outliers final: 19 residues processed: 183 average time/residue: 0.0788 time to fit residues: 22.4344 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 : 0.327 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 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 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 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 Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.139676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101873 restraints weight = 19587.500| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.78 r_work: 0.3341 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11000 Z= 0.138 Angle : 0.699 13.243 15028 Z= 0.325 Chirality : 0.047 0.496 1752 Planarity : 0.004 0.046 1802 Dihedral : 12.297 112.930 2158 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.33 % Favored : 94.51 % Rotamer: Outliers : 3.62 % Allowed : 27.56 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.24), residues: 1256 helix: 1.80 (0.21), residues: 578 sheet: 0.64 (0.32), residues: 280 loop : -2.28 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 172 TYR 0.049 0.001 TYR A 717 PHE 0.024 0.001 PHE A 445 TRP 0.023 0.001 TRP A 446 HIS 0.007 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00313 (10976) covalent geometry : angle 0.63770 (14980) SS BOND : bond 0.00203 ( 6) SS BOND : angle 0.74683 ( 12) hydrogen bonds : bond 0.04420 ( 615) hydrogen bonds : angle 4.46277 ( 1758) metal coordination : bond 0.00205 ( 6) link_BETA1-4 : bond 0.00503 ( 4) link_BETA1-4 : angle 2.95199 ( 12) link_NAG-ASN : bond 0.01000 ( 8) link_NAG-ASN : angle 6.88348 ( 24) *********************** 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: 41 poor density : 154 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5480 (mt) REVERT: A 605 TYR cc_start: 0.8580 (m-80) cc_final: 0.8365 (m-80) REVERT: A 713 ASP cc_start: 0.8037 (t0) cc_final: 0.7795 (t0) REVERT: B 208 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.5469 (ppp) REVERT: B 613 MET cc_start: 0.8597 (mmm) cc_final: 0.8361 (mmm) REVERT: B 722 PHE cc_start: 0.8644 (m-10) cc_final: 0.8391 (m-10) REVERT: B 736 MET cc_start: 0.8144 (mmt) cc_final: 0.7885 (mmt) REVERT: B 767 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7841 (m-80) outliers start: 41 outliers final: 20 residues processed: 188 average time/residue: 0.0707 time to fit residues: 21.0382 Evaluate side-chains 162 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 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 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 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 536 TYR Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 59 optimal weight: 0.0970 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.138452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.101028 restraints weight = 19989.376| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.75 r_work: 0.3340 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11000 Z= 0.174 Angle : 0.721 13.864 15028 Z= 0.335 Chirality : 0.048 0.507 1752 Planarity : 0.004 0.045 1802 Dihedral : 11.892 113.541 2156 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.61 % Favored : 93.23 % Rotamer: Outliers : 4.86 % Allowed : 28.53 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.24), residues: 1256 helix: 1.70 (0.21), residues: 576 sheet: 0.81 (0.33), residues: 268 loop : -2.42 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 524 TYR 0.033 0.001 TYR A 717 PHE 0.022 0.001 PHE B 705 TRP 0.024 0.001 TRP A 446 HIS 0.006 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00403 (10976) covalent geometry : angle 0.66139 (14980) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.90388 ( 12) hydrogen bonds : bond 0.04639 ( 615) hydrogen bonds : angle 4.54278 ( 1758) metal coordination : bond 0.00304 ( 6) link_BETA1-4 : bond 0.00469 ( 4) link_BETA1-4 : angle 2.92981 ( 12) link_NAG-ASN : bond 0.01046 ( 8) link_NAG-ASN : angle 6.91336 ( 24) *********************** 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 203 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: A 326 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5199 (mt) REVERT: A 455 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: A 702 PHE cc_start: 0.8081 (m-80) cc_final: 0.7407 (m-80) REVERT: A 713 ASP cc_start: 0.8093 (t0) cc_final: 0.7844 (t0) REVERT: B 36 ARG cc_start: 0.5015 (OUTLIER) cc_final: 0.3400 (mtt180) REVERT: B 160 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7689 (mttp) REVERT: B 208 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.5551 (ppp) REVERT: B 454 PHE cc_start: 0.8413 (m-80) cc_final: 0.7828 (m-80) REVERT: B 613 MET cc_start: 0.8592 (mmm) cc_final: 0.8346 (mmm) REVERT: B 722 PHE cc_start: 0.8746 (m-10) cc_final: 0.8469 (m-10) REVERT: B 736 MET cc_start: 0.8114 (mmt) cc_final: 0.7840 (mmt) REVERT: B 767 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7785 (m-80) outliers start: 55 outliers final: 31 residues processed: 191 average time/residue: 0.0750 time to fit residues: 22.6505 Evaluate side-chains 181 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 164 THR Chi-restraints excluded: chain A residue 173 THR 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 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 723 ILE 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 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 536 TYR Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.138239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101157 restraints weight = 19724.976| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.75 r_work: 0.3337 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1807 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= 0.180 Angle : 0.723 14.181 15028 Z= 0.337 Chirality : 0.048 0.511 1752 Planarity : 0.004 0.045 1802 Dihedral : 11.539 113.896 2156 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.45 % Favored : 93.39 % Rotamer: Outliers : 5.57 % Allowed : 27.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.24), residues: 1256 helix: 1.84 (0.22), residues: 552 sheet: 0.79 (0.33), residues: 268 loop : -2.39 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 524 TYR 0.030 0.002 TYR A 717 PHE 0.022 0.001 PHE B 705 TRP 0.028 0.002 TRP A 446 HIS 0.005 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00415 (10976) covalent geometry : angle 0.66205 (14980) SS BOND : bond 0.00214 ( 6) SS BOND : angle 0.99330 ( 12) hydrogen bonds : bond 0.04674 ( 615) hydrogen bonds : angle 4.52763 ( 1758) metal coordination : bond 0.00338 ( 6) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 3.04455 ( 12) link_NAG-ASN : bond 0.01072 ( 8) link_NAG-ASN : angle 6.97834 ( 24) *********************** 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 213 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 150 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: A 326 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5216 (mt) REVERT: A 455 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: A 702 PHE cc_start: 0.8138 (m-80) cc_final: 0.7635 (m-80) REVERT: A 713 ASP cc_start: 0.8126 (t0) cc_final: 0.7876 (t0) REVERT: B 36 ARG cc_start: 0.4993 (OUTLIER) cc_final: 0.3414 (mtt180) REVERT: B 160 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7706 (mttp) REVERT: B 208 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.5565 (ppp) REVERT: B 454 PHE cc_start: 0.8475 (m-80) cc_final: 0.7914 (m-80) REVERT: B 580 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7348 (tpp) REVERT: B 613 MET cc_start: 0.8615 (mmm) cc_final: 0.8328 (mmm) REVERT: B 722 PHE cc_start: 0.8785 (m-10) cc_final: 0.8477 (m-10) REVERT: B 736 MET cc_start: 0.8122 (mmt) cc_final: 0.7825 (mmt) REVERT: B 767 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7878 (m-80) outliers start: 63 outliers final: 42 residues processed: 194 average time/residue: 0.0808 time to fit residues: 24.8318 Evaluate side-chains 190 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 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 686 MET 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 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 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 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 512 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.139740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.102595 restraints weight = 19727.308| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.72 r_work: 0.3368 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11000 Z= 0.134 Angle : 0.709 13.960 15028 Z= 0.324 Chirality : 0.047 0.513 1752 Planarity : 0.004 0.048 1802 Dihedral : 11.226 113.380 2156 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.57 % Favored : 94.27 % Rotamer: Outliers : 4.15 % Allowed : 29.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.24), residues: 1256 helix: 1.89 (0.22), residues: 552 sheet: 0.93 (0.34), residues: 268 loop : -2.39 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 524 TYR 0.020 0.001 TYR A 717 PHE 0.024 0.001 PHE A 445 TRP 0.033 0.001 TRP A 446 HIS 0.005 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00296 (10976) covalent geometry : angle 0.64737 (14980) SS BOND : bond 0.00203 ( 6) SS BOND : angle 0.97281 ( 12) hydrogen bonds : bond 0.04377 ( 615) hydrogen bonds : angle 4.44514 ( 1758) metal coordination : bond 0.00166 ( 6) link_BETA1-4 : bond 0.00368 ( 4) link_BETA1-4 : angle 3.17782 ( 12) link_NAG-ASN : bond 0.01094 ( 8) link_NAG-ASN : angle 6.88409 ( 24) *********************** 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 198 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.5873 (OUTLIER) cc_final: 0.5331 (mt) REVERT: A 455 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: A 702 PHE cc_start: 0.8013 (m-80) cc_final: 0.7550 (m-80) REVERT: A 713 ASP cc_start: 0.8100 (t0) cc_final: 0.7800 (t0) REVERT: B 36 ARG cc_start: 0.4902 (OUTLIER) cc_final: 0.3460 (mtt-85) REVERT: B 160 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7845 (mttp) REVERT: B 208 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.5488 (ppp) REVERT: B 454 PHE cc_start: 0.8383 (m-80) cc_final: 0.7894 (m-80) REVERT: B 613 MET cc_start: 0.8595 (mmm) cc_final: 0.8322 (mmm) REVERT: B 722 PHE cc_start: 0.8761 (m-10) cc_final: 0.8431 (m-10) REVERT: B 736 MET cc_start: 0.8139 (mmt) cc_final: 0.7818 (mmt) REVERT: B 767 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7878 (m-80) outliers start: 47 outliers final: 33 residues processed: 187 average time/residue: 0.0703 time to fit residues: 21.0251 Evaluate side-chains 182 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 292 ASN 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 491 VAL 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 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 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 512 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 482 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.139604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.103300 restraints weight = 20435.271| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.99 r_work: 0.3405 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11000 Z= 0.296 Angle : 0.838 14.991 15028 Z= 0.398 Chirality : 0.052 0.575 1752 Planarity : 0.005 0.048 1802 Dihedral : 11.351 115.068 2156 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.40 % Favored : 92.44 % Rotamer: Outliers : 5.65 % Allowed : 27.30 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.24), residues: 1256 helix: 1.56 (0.22), residues: 554 sheet: 0.48 (0.33), residues: 270 loop : -2.41 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.046 0.002 TYR A 717 PHE 0.028 0.002 PHE A 808 TRP 0.027 0.002 TRP A 446 HIS 0.007 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00691 (10976) covalent geometry : angle 0.78177 (14980) SS BOND : bond 0.00286 ( 6) SS BOND : angle 1.17714 ( 12) hydrogen bonds : bond 0.05424 ( 615) hydrogen bonds : angle 4.76215 ( 1758) metal coordination : bond 0.00539 ( 6) link_BETA1-4 : bond 0.00368 ( 4) link_BETA1-4 : angle 3.10684 ( 12) link_NAG-ASN : bond 0.01126 ( 8) link_NAG-ASN : angle 7.29355 ( 24) *********************** 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 205 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 141 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: A 455 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: A 702 PHE cc_start: 0.8032 (m-80) cc_final: 0.7616 (m-80) REVERT: A 713 ASP cc_start: 0.8092 (t0) cc_final: 0.7824 (t0) REVERT: B 36 ARG cc_start: 0.5117 (OUTLIER) cc_final: 0.3454 (mtt-85) REVERT: B 160 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7923 (mttp) REVERT: B 208 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.5703 (ppp) REVERT: B 210 TYR cc_start: 0.7198 (t80) cc_final: 0.6797 (t80) REVERT: B 536 TYR cc_start: 0.6682 (OUTLIER) cc_final: 0.6474 (t80) REVERT: B 613 MET cc_start: 0.8578 (mmm) cc_final: 0.8278 (mmm) REVERT: B 722 PHE cc_start: 0.8811 (m-10) cc_final: 0.8492 (m-10) REVERT: B 736 MET cc_start: 0.8187 (mmt) cc_final: 0.7845 (mmt) REVERT: B 767 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7983 (m-80) outliers start: 64 outliers final: 47 residues processed: 186 average time/residue: 0.0785 time to fit residues: 23.3995 Evaluate side-chains 191 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 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 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 686 MET Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 719 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 757 VAL Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.139843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103968 restraints weight = 19858.262| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.72 r_work: 0.3420 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11000 Z= 0.161 Angle : 0.753 14.474 15028 Z= 0.346 Chirality : 0.048 0.539 1752 Planarity : 0.004 0.043 1802 Dihedral : 11.069 114.165 2156 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 4.59 % Allowed : 28.27 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.24), residues: 1256 helix: 1.75 (0.22), residues: 552 sheet: 0.50 (0.33), residues: 280 loop : -2.42 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.044 0.001 TYR A 717 PHE 0.025 0.001 PHE A 445 TRP 0.024 0.002 TRP A 446 HIS 0.005 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00364 (10976) covalent geometry : angle 0.69195 (14980) SS BOND : bond 0.00220 ( 6) SS BOND : angle 1.01145 ( 12) hydrogen bonds : bond 0.04744 ( 615) hydrogen bonds : angle 4.53953 ( 1758) metal coordination : bond 0.00242 ( 6) link_BETA1-4 : bond 0.00255 ( 4) link_BETA1-4 : angle 3.31411 ( 12) link_NAG-ASN : bond 0.01104 ( 8) link_NAG-ASN : angle 7.07863 ( 24) *********************** 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 199 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: A 455 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: A 702 PHE cc_start: 0.7973 (m-80) cc_final: 0.7500 (m-80) REVERT: A 713 ASP cc_start: 0.8116 (t0) cc_final: 0.7716 (t0) REVERT: B 36 ARG cc_start: 0.5017 (OUTLIER) cc_final: 0.3492 (mtt-85) REVERT: B 160 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7966 (mttp) REVERT: B 208 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.5564 (ppp) REVERT: B 221 MET cc_start: 0.8006 (mmm) cc_final: 0.7806 (mmm) REVERT: B 536 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.6472 (t80) REVERT: B 722 PHE cc_start: 0.8790 (m-10) cc_final: 0.8497 (m-10) REVERT: B 736 MET cc_start: 0.8231 (mmt) cc_final: 0.7889 (mmt) REVERT: B 767 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8024 (m-80) outliers start: 52 outliers final: 39 residues processed: 187 average time/residue: 0.0783 time to fit residues: 23.2487 Evaluate side-chains 187 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 506 LEU 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 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 767 PHE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 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 791 ASP 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 14 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.141453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105833 restraints weight = 19735.344| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.60 r_work: 0.3454 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11000 Z= 0.135 Angle : 0.739 14.146 15028 Z= 0.335 Chirality : 0.047 0.522 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.733 113.143 2156 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.57 % Favored : 94.27 % Rotamer: Outliers : 3.98 % Allowed : 29.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.24), residues: 1256 helix: 1.86 (0.22), residues: 552 sheet: 0.76 (0.33), residues: 268 loop : -2.41 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.019 0.001 TYR A 188 PHE 0.024 0.001 PHE A 445 TRP 0.027 0.002 TRP A 446 HIS 0.005 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00300 (10976) covalent geometry : angle 0.67811 (14980) SS BOND : bond 0.00207 ( 6) SS BOND : angle 0.97396 ( 12) hydrogen bonds : bond 0.04328 ( 615) hydrogen bonds : angle 4.42419 ( 1758) metal coordination : bond 0.00191 ( 6) link_BETA1-4 : bond 0.00243 ( 4) link_BETA1-4 : angle 3.44869 ( 12) link_NAG-ASN : bond 0.01086 ( 8) link_NAG-ASN : angle 6.97587 ( 24) *********************** 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 193 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: A 455 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: A 555 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8247 (tp30) REVERT: A 689 MET cc_start: 0.8867 (mmt) cc_final: 0.8621 (mmp) REVERT: A 702 PHE cc_start: 0.8006 (m-80) cc_final: 0.7558 (m-80) REVERT: B 36 ARG cc_start: 0.4884 (OUTLIER) cc_final: 0.3429 (mtt-85) REVERT: B 208 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.5343 (ppp) REVERT: B 221 MET cc_start: 0.7905 (mmm) cc_final: 0.7693 (mmm) REVERT: B 613 MET cc_start: 0.8578 (mmm) cc_final: 0.8253 (mmm) REVERT: B 722 PHE cc_start: 0.8759 (m-10) cc_final: 0.8440 (m-10) REVERT: B 736 MET cc_start: 0.8252 (mmt) cc_final: 0.7893 (mmt) REVERT: B 767 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7853 (m-80) outliers start: 45 outliers final: 34 residues processed: 183 average time/residue: 0.0781 time to fit residues: 22.8350 Evaluate side-chains 178 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 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 767 PHE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 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 816 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.141563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103749 restraints weight = 19717.583| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.05 r_work: 0.3475 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11000 Z= 0.138 Angle : 0.740 14.046 15028 Z= 0.338 Chirality : 0.047 0.520 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.581 112.823 2156 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 3.45 % Allowed : 29.95 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.24), residues: 1256 helix: 1.86 (0.22), residues: 552 sheet: 0.87 (0.34), residues: 268 loop : -2.35 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.022 0.001 TYR A 717 PHE 0.025 0.001 PHE B 705 TRP 0.046 0.002 TRP B 446 HIS 0.004 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00309 (10976) covalent geometry : angle 0.67978 (14980) SS BOND : bond 0.00219 ( 6) SS BOND : angle 0.95923 ( 12) hydrogen bonds : bond 0.04313 ( 615) hydrogen bonds : angle 4.38124 ( 1758) metal coordination : bond 0.00173 ( 6) link_BETA1-4 : bond 0.00259 ( 4) link_BETA1-4 : angle 3.47985 ( 12) link_NAG-ASN : bond 0.01084 ( 8) link_NAG-ASN : angle 6.94361 ( 24) ********************** 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 178 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: A 455 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: A 555 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8214 (tp30) REVERT: A 689 MET cc_start: 0.8846 (mmt) cc_final: 0.8598 (mmp) REVERT: A 702 PHE cc_start: 0.7919 (m-80) cc_final: 0.7478 (m-80) REVERT: B 36 ARG cc_start: 0.4843 (OUTLIER) cc_final: 0.3422 (mtt-85) REVERT: B 208 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.5353 (ppp) REVERT: B 221 MET cc_start: 0.7839 (mmm) cc_final: 0.7633 (mmm) REVERT: B 613 MET cc_start: 0.8573 (mmm) cc_final: 0.8236 (mmm) REVERT: B 722 PHE cc_start: 0.8765 (m-10) cc_final: 0.8455 (m-10) REVERT: B 736 MET cc_start: 0.8255 (mmt) cc_final: 0.7897 (mmt) REVERT: B 767 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7897 (m-80) outliers start: 39 outliers final: 33 residues processed: 168 average time/residue: 0.0750 time to fit residues: 20.4155 Evaluate side-chains 175 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER 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 744 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 767 PHE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 310 SER 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 500 SER Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 101 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.141448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105168 restraints weight = 19890.158| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.59 r_work: 0.3449 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2504 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= 0.143 Angle : 0.742 14.142 15028 Z= 0.337 Chirality : 0.047 0.524 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.437 112.682 2156 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 3.62 % Allowed : 29.95 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.24), residues: 1256 helix: 1.90 (0.22), residues: 552 sheet: 0.84 (0.34), residues: 268 loop : -2.34 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.021 0.001 TYR A 188 PHE 0.023 0.001 PHE A 445 TRP 0.041 0.002 TRP B 446 HIS 0.004 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00322 (10976) covalent geometry : angle 0.68137 (14980) SS BOND : bond 0.00207 ( 6) SS BOND : angle 0.92937 ( 12) hydrogen bonds : bond 0.04277 ( 615) hydrogen bonds : angle 4.36806 ( 1758) metal coordination : bond 0.00216 ( 6) link_BETA1-4 : bond 0.00230 ( 4) link_BETA1-4 : angle 3.51789 ( 12) link_NAG-ASN : bond 0.01076 ( 8) link_NAG-ASN : angle 6.94328 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2469.11 seconds wall clock time: 43 minutes 14.82 seconds (2594.82 seconds total)