Starting phenix.real_space_refine on Tue May 13 16:52:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wot_37698/05_2025/8wot_37698_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wot_37698/05_2025/8wot_37698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wot_37698/05_2025/8wot_37698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wot_37698/05_2025/8wot_37698.map" model { file = "/net/cci-nas-00/data/ceres_data/8wot_37698/05_2025/8wot_37698_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wot_37698/05_2025/8wot_37698_neut.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10672 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 Chain: "B" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.02, per 1000 atoms: 0.66 Number of scatterers: 10672 At special positions: 0 Unit cell: (98.716, 86.802, 137.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 58 16.00 O 1862 8.00 N 1644 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 67 " " NAG A 902 " - " ASN A 136 " " NAG B 901 " - " ASN B 67 " " NAG B 902 " - " ASN B 136 " " NAG C 1 " - " ASN A 83 " " NAG D 1 " - " ASN A 57 " " NAG E 1 " - " ASN B 83 " " NAG F 1 " - " ASN B 57 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 907 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 907 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 800 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 796 " 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: 34 helices and 10 sheets defined 49.8% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 302 through 336 removed outlier: 3.871A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 3.975A 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: 3.989A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.925A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 529 removed outlier: 3.927A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.607A pdb=" N GLU A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 3.557A pdb=" N TYR A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.928A pdb=" N PHE A 571 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 594 removed outlier: 3.812A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 622 removed outlier: 3.898A 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: 3.700A 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 'B' and resid 38 through 43 removed outlier: 3.517A pdb=" N ALA B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) 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: 3.777A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 474 removed outlier: 3.549A 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: 3.997A 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: 3.879A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 508 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.563A pdb=" N GLU B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 removed outlier: 3.782A pdb=" N VAL B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 4.086A pdb=" N PHE B 571 " --> pdb=" O TYR B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 3.853A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 622 removed outlier: 3.773A 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: 3.647A pdb=" N GLN B 768 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 794 through 817 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: 4.753A 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 62 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: 4.765A 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 181 612 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3170 1.34 - 1.46: 2831 1.46 - 1.58: 4885 1.58 - 1.70: 0 1.70 - 1.81: 90 Bond restraints: 10976 Sorted by residual: bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 ... (remaining 10971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 14892 2.62 - 5.25: 83 5.25 - 7.87: 3 7.87 - 10.50: 0 10.50 - 13.12: 2 Bond angle restraints: 14980 Sorted by residual: angle pdb=" C SER A 600 " pdb=" CA SER A 600 " pdb=" CB SER A 600 " ideal model delta sigma weight residual 116.54 110.44 6.10 1.15e+00 7.56e-01 2.81e+01 angle pdb=" C SER B 600 " pdb=" CA SER B 600 " pdb=" CB SER B 600 " ideal model delta sigma weight residual 116.54 110.48 6.06 1.15e+00 7.56e-01 2.78e+01 angle pdb=" CA LEU B 789 " pdb=" CB LEU B 789 " pdb=" CG LEU B 789 " ideal model delta sigma weight residual 116.30 129.42 -13.12 3.50e+00 8.16e-02 1.41e+01 angle pdb=" CA SER A 600 " pdb=" C SER A 600 " pdb=" N ALA A 601 " ideal model delta sigma weight residual 119.52 116.57 2.95 7.90e-01 1.60e+00 1.39e+01 angle pdb=" CA SER B 600 " pdb=" C SER B 600 " pdb=" N ALA B 601 " ideal model delta sigma weight residual 119.52 116.63 2.89 7.90e-01 1.60e+00 1.33e+01 ... (remaining 14975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.66: 6356 25.66 - 51.33: 481 51.33 - 76.99: 59 76.99 - 102.66: 22 102.66 - 128.32: 10 Dihedral angle restraints: 6928 sinusoidal: 3148 harmonic: 3780 Sorted by residual: 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 65.36 -128.32 1 3.00e+01 1.11e-03 1.73e+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 65.32 -128.28 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C2 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sinusoidal sigma weight residual 175.11 62.53 112.58 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1596 0.069 - 0.138: 151 0.138 - 0.207: 3 0.207 - 0.276: 0 0.276 - 0.345: 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 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+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 -2.07 -0.33 2.00e-01 2.50e+01 2.72e+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 -2.21 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 1749 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 83 " 0.002 2.00e-02 2.50e+03 1.90e-02 4.50e+00 pdb=" CG ASN B 83 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 83 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 83 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 747 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO B 748 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 748 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 748 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 747 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 748 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 748 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 748 " -0.023 5.00e-02 4.00e+02 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 113 2.60 - 3.17: 9668 3.17 - 3.75: 15866 3.75 - 4.32: 20935 4.32 - 4.90: 35956 Nonbonded interactions: 82538 Sorted by model distance: nonbonded pdb=" OG SER B 701 " pdb=" OH TYR B 717 " model vdw 2.020 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 2.073 3.040 nonbonded pdb=" OG SER A 740 " pdb=" OE2 GLU A 742 " model vdw 2.097 3.040 nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 2.103 3.040 nonbonded pdb=" N GLU B 137 " pdb=" OE1 GLU B 137 " model vdw 2.121 3.120 ... (remaining 82533 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.530 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 0.052 11000 Z= 0.148 Angle : 0.552 13.124 15028 Z= 0.280 Chirality : 0.040 0.345 1752 Planarity : 0.003 0.045 1802 Dihedral : 17.953 128.319 4470 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 30.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.27 % Allowed : 29.86 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1256 helix: 3.00 (0.21), residues: 580 sheet: 0.62 (0.33), residues: 268 loop : -2.36 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 446 HIS 0.001 0.000 HIS B 636 PHE 0.025 0.001 PHE B 705 TYR 0.016 0.001 TYR B 709 ARG 0.002 0.000 ARG B 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 8) link_NAG-ASN : angle 4.60749 ( 24) link_BETA1-4 : bond 0.00181 ( 4) link_BETA1-4 : angle 1.61689 ( 12) hydrogen bonds : bond 0.09038 ( 612) hydrogen bonds : angle 4.77355 ( 1758) metal coordination : bond 0.00164 ( 6) SS BOND : bond 0.00102 ( 6) SS BOND : angle 0.41807 ( 12) covalent geometry : bond 0.00303 (10976) covalent geometry : angle 0.51892 (14980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 689 MET cc_start: 0.8366 (pmm) cc_final: 0.7892 (pmm) outliers start: 3 outliers final: 2 residues processed: 130 average time/residue: 0.1902 time to fit residues: 37.3720 Evaluate side-chains 131 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 714 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 30.0000 chunk 60 optimal weight: 0.0030 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 796 HIS B 74 GLN B 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.143464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097763 restraints weight = 17061.928| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.82 r_work: 0.3335 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.901 11000 Z= 0.359 Angle : 0.734 13.210 15028 Z= 0.349 Chirality : 0.050 0.556 1752 Planarity : 0.004 0.051 1802 Dihedral : 12.627 111.409 2158 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.09 % Favored : 92.75 % Rotamer: Outliers : 3.09 % Allowed : 25.44 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1256 helix: 2.04 (0.21), residues: 586 sheet: 0.43 (0.31), residues: 280 loop : -2.57 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 106 HIS 0.002 0.001 HIS A 800 PHE 0.025 0.002 PHE A 705 TYR 0.034 0.002 TYR A 717 ARG 0.004 0.001 ARG A 781 Details of bonding type rmsd link_NAG-ASN : bond 0.00769 ( 8) link_NAG-ASN : angle 7.00371 ( 24) link_BETA1-4 : bond 0.00509 ( 4) link_BETA1-4 : angle 2.71450 ( 12) hydrogen bonds : bond 0.04832 ( 612) hydrogen bonds : angle 4.56019 ( 1758) metal coordination : bond 0.36772 ( 6) SS BOND : bond 0.00170 ( 6) SS BOND : angle 0.87233 ( 12) covalent geometry : bond 0.00514 (10976) covalent geometry : angle 0.67494 (14980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6984 (tt) REVERT: A 520 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8408 (tp) REVERT: A 540 LYS cc_start: 0.6312 (tmtt) cc_final: 0.5917 (tmtt) REVERT: A 586 MET cc_start: 0.8147 (mmp) cc_final: 0.7923 (mmp) outliers start: 35 outliers final: 20 residues processed: 162 average time/residue: 0.1767 time to fit residues: 43.7387 Evaluate side-chains 154 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 750 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 107 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.147239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100715 restraints weight = 17199.304| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.00 r_work: 0.3356 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11000 Z= 0.124 Angle : 0.676 12.900 15028 Z= 0.314 Chirality : 0.047 0.538 1752 Planarity : 0.004 0.050 1802 Dihedral : 11.728 108.939 2154 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.78 % Favored : 95.06 % Rotamer: Outliers : 3.45 % Allowed : 25.27 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1256 helix: 1.93 (0.21), residues: 590 sheet: 0.69 (0.32), residues: 272 loop : -2.46 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 446 HIS 0.004 0.001 HIS A 563 PHE 0.030 0.001 PHE B 705 TYR 0.036 0.001 TYR B 717 ARG 0.003 0.000 ARG A 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00913 ( 8) link_NAG-ASN : angle 6.78617 ( 24) link_BETA1-4 : bond 0.00533 ( 4) link_BETA1-4 : angle 3.03288 ( 12) hydrogen bonds : bond 0.04193 ( 612) hydrogen bonds : angle 4.34733 ( 1758) metal coordination : bond 0.00899 ( 6) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.55952 ( 12) covalent geometry : bond 0.00264 (10976) covalent geometry : angle 0.61413 (14980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6898 (tt) REVERT: A 520 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8394 (tp) REVERT: A 540 LYS cc_start: 0.6172 (tmtt) cc_final: 0.5595 (tmtt) REVERT: A 580 MET cc_start: 0.8083 (tpp) cc_final: 0.7642 (tpp) REVERT: A 722 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8802 (m-10) outliers start: 39 outliers final: 19 residues processed: 165 average time/residue: 0.1754 time to fit residues: 44.0639 Evaluate side-chains 152 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 750 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 28 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.143216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097319 restraints weight = 16857.490| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.92 r_work: 0.3323 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11000 Z= 0.191 Angle : 0.717 13.655 15028 Z= 0.336 Chirality : 0.048 0.550 1752 Planarity : 0.004 0.051 1802 Dihedral : 11.374 108.644 2154 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.69 % Favored : 93.15 % Rotamer: Outliers : 4.06 % Allowed : 25.35 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1256 helix: 1.79 (0.21), residues: 586 sheet: 0.66 (0.32), residues: 268 loop : -2.54 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 446 HIS 0.003 0.001 HIS A 636 PHE 0.025 0.001 PHE B 705 TYR 0.030 0.002 TYR A 717 ARG 0.003 0.000 ARG A 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00877 ( 8) link_NAG-ASN : angle 7.07457 ( 24) link_BETA1-4 : bond 0.00551 ( 4) link_BETA1-4 : angle 3.03203 ( 12) hydrogen bonds : bond 0.04596 ( 612) hydrogen bonds : angle 4.40635 ( 1758) metal coordination : bond 0.00861 ( 6) SS BOND : bond 0.00175 ( 6) SS BOND : angle 0.72973 ( 12) covalent geometry : bond 0.00452 (10976) covalent geometry : angle 0.65402 (14980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6941 (tt) REVERT: A 520 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8431 (tp) REVERT: A 540 LYS cc_start: 0.6354 (tmtt) cc_final: 0.5747 (tmtt) REVERT: B 686 MET cc_start: 0.5686 (pmm) cc_final: 0.5200 (pmm) outliers start: 46 outliers final: 34 residues processed: 167 average time/residue: 0.1818 time to fit residues: 46.1888 Evaluate side-chains 167 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 0.0870 chunk 91 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN B 501 ASN B 796 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.146253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100734 restraints weight = 16741.339| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.91 r_work: 0.3371 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.879 11000 Z= 0.303 Angle : 0.684 13.451 15028 Z= 0.312 Chirality : 0.046 0.532 1752 Planarity : 0.004 0.049 1802 Dihedral : 10.978 107.850 2154 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.62 % Favored : 95.22 % Rotamer: Outliers : 3.53 % Allowed : 26.24 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1256 helix: 1.78 (0.21), residues: 594 sheet: 0.89 (0.33), residues: 260 loop : -2.47 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 446 HIS 0.004 0.001 HIS A 636 PHE 0.031 0.001 PHE B 705 TYR 0.031 0.001 TYR A 717 ARG 0.003 0.000 ARG A 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00991 ( 8) link_NAG-ASN : angle 6.83787 ( 24) link_BETA1-4 : bond 0.00483 ( 4) link_BETA1-4 : angle 3.21557 ( 12) hydrogen bonds : bond 0.04007 ( 612) hydrogen bonds : angle 4.29009 ( 1758) metal coordination : bond 0.35871 ( 6) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.51464 ( 12) covalent geometry : bond 0.00250 (10976) covalent geometry : angle 0.62096 (14980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6827 (tt) REVERT: A 520 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8451 (tp) REVERT: A 540 LYS cc_start: 0.6143 (tmtt) cc_final: 0.5400 (tmtt) outliers start: 40 outliers final: 29 residues processed: 174 average time/residue: 0.1961 time to fit residues: 51.2247 Evaluate side-chains 160 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.142637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.096531 restraints weight = 16868.317| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.94 r_work: 0.3307 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11000 Z= 0.235 Angle : 0.763 14.193 15028 Z= 0.357 Chirality : 0.050 0.563 1752 Planarity : 0.004 0.049 1802 Dihedral : 10.819 108.021 2154 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.93 % Favored : 92.91 % Rotamer: Outliers : 4.24 % Allowed : 26.24 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1256 helix: 1.69 (0.21), residues: 586 sheet: 0.61 (0.32), residues: 268 loop : -2.60 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 446 HIS 0.013 0.001 HIS B 800 PHE 0.033 0.002 PHE B 705 TYR 0.040 0.002 TYR A 717 ARG 0.004 0.000 ARG A 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00860 ( 8) link_NAG-ASN : angle 7.27970 ( 24) link_BETA1-4 : bond 0.00602 ( 4) link_BETA1-4 : angle 3.17298 ( 12) hydrogen bonds : bond 0.04859 ( 612) hydrogen bonds : angle 4.43379 ( 1758) metal coordination : bond 0.01455 ( 6) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.78473 ( 12) covalent geometry : bond 0.00561 (10976) covalent geometry : angle 0.70075 (14980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6904 (tt) REVERT: A 520 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8494 (tp) REVERT: B 686 MET cc_start: 0.5703 (pmm) cc_final: 0.4787 (pmm) outliers start: 48 outliers final: 38 residues processed: 177 average time/residue: 0.1909 time to fit residues: 51.0939 Evaluate side-chains 171 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU 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 516 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.144807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098879 restraints weight = 16874.226| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.95 r_work: 0.3344 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11000 Z= 0.142 Angle : 0.727 13.929 15028 Z= 0.332 Chirality : 0.047 0.543 1752 Planarity : 0.004 0.048 1802 Dihedral : 10.621 107.946 2154 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 3.89 % Allowed : 27.12 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1256 helix: 1.67 (0.21), residues: 592 sheet: 0.79 (0.32), residues: 260 loop : -2.58 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.035 0.001 PHE B 705 TYR 0.038 0.001 TYR A 717 ARG 0.004 0.000 ARG A 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00959 ( 8) link_NAG-ASN : angle 7.05911 ( 24) link_BETA1-4 : bond 0.00407 ( 4) link_BETA1-4 : angle 3.25131 ( 12) hydrogen bonds : bond 0.04346 ( 612) hydrogen bonds : angle 4.33166 ( 1758) metal coordination : bond 0.00621 ( 6) SS BOND : bond 0.00176 ( 6) SS BOND : angle 0.53284 ( 12) covalent geometry : bond 0.00321 (10976) covalent geometry : angle 0.66412 (14980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6832 (tt) REVERT: A 520 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8506 (tp) outliers start: 44 outliers final: 32 residues processed: 170 average time/residue: 0.1841 time to fit residues: 47.7898 Evaluate side-chains 165 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.145093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.101282 restraints weight = 16672.961| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.69 r_work: 0.3321 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11000 Z= 0.139 Angle : 0.727 13.920 15028 Z= 0.331 Chirality : 0.047 0.541 1752 Planarity : 0.004 0.046 1802 Dihedral : 10.476 107.706 2154 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.97 % Favored : 93.87 % Rotamer: Outliers : 3.18 % Allowed : 27.47 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1256 helix: 1.68 (0.21), residues: 590 sheet: 0.78 (0.32), residues: 268 loop : -2.57 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.039 0.001 PHE A 705 TYR 0.037 0.001 TYR A 717 ARG 0.005 0.000 ARG B 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00965 ( 8) link_NAG-ASN : angle 7.06936 ( 24) link_BETA1-4 : bond 0.00411 ( 4) link_BETA1-4 : angle 3.29726 ( 12) hydrogen bonds : bond 0.04245 ( 612) hydrogen bonds : angle 4.31599 ( 1758) metal coordination : bond 0.00444 ( 6) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.56648 ( 12) covalent geometry : bond 0.00315 (10976) covalent geometry : angle 0.66436 (14980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6890 (tt) REVERT: A 520 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8498 (tp) outliers start: 36 outliers final: 32 residues processed: 161 average time/residue: 0.1818 time to fit residues: 44.6481 Evaluate side-chains 163 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 103 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.146172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100417 restraints weight = 16847.290| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.95 r_work: 0.3368 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1818 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= 0.124 Angle : 0.725 13.855 15028 Z= 0.328 Chirality : 0.047 0.534 1752 Planarity : 0.004 0.046 1802 Dihedral : 10.284 107.141 2154 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.94 % Favored : 94.90 % Rotamer: Outliers : 3.09 % Allowed : 27.83 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1256 helix: 1.80 (0.21), residues: 580 sheet: 0.88 (0.32), residues: 268 loop : -2.54 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 446 HIS 0.003 0.000 HIS A 636 PHE 0.046 0.001 PHE A 705 TYR 0.036 0.001 TYR A 717 ARG 0.006 0.000 ARG B 712 Details of bonding type rmsd link_NAG-ASN : bond 0.01006 ( 8) link_NAG-ASN : angle 6.97886 ( 24) link_BETA1-4 : bond 0.00349 ( 4) link_BETA1-4 : angle 3.36486 ( 12) hydrogen bonds : bond 0.03992 ( 612) hydrogen bonds : angle 4.26108 ( 1758) metal coordination : bond 0.00309 ( 6) SS BOND : bond 0.00161 ( 6) SS BOND : angle 0.54112 ( 12) covalent geometry : bond 0.00272 (10976) covalent geometry : angle 0.66349 (14980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6829 (tt) REVERT: A 520 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8554 (tp) outliers start: 35 outliers final: 30 residues processed: 159 average time/residue: 0.2045 time to fit residues: 49.8418 Evaluate side-chains 161 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 0.8980 chunk 20 optimal weight: 0.0470 chunk 59 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 118 optimal weight: 0.0470 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.146342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.100754 restraints weight = 16806.089| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.93 r_work: 0.3384 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11000 Z= 0.123 Angle : 0.730 13.755 15028 Z= 0.328 Chirality : 0.047 0.534 1752 Planarity : 0.004 0.046 1802 Dihedral : 10.164 106.776 2154 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 2.74 % Allowed : 28.53 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1256 helix: 1.78 (0.21), residues: 580 sheet: 0.94 (0.32), residues: 268 loop : -2.50 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 446 HIS 0.003 0.001 HIS B 636 PHE 0.049 0.001 PHE A 705 TYR 0.036 0.001 TYR A 717 ARG 0.007 0.000 ARG B 712 Details of bonding type rmsd link_NAG-ASN : bond 0.01008 ( 8) link_NAG-ASN : angle 6.95074 ( 24) link_BETA1-4 : bond 0.00339 ( 4) link_BETA1-4 : angle 3.40226 ( 12) hydrogen bonds : bond 0.03938 ( 612) hydrogen bonds : angle 4.22589 ( 1758) metal coordination : bond 0.00285 ( 6) SS BOND : bond 0.00155 ( 6) SS BOND : angle 0.55341 ( 12) covalent geometry : bond 0.00272 (10976) covalent geometry : angle 0.66918 (14980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6832 (tt) REVERT: A 520 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8580 (tp) outliers start: 31 outliers final: 29 residues processed: 155 average time/residue: 0.1867 time to fit residues: 43.5417 Evaluate side-chains 163 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 750 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.145434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.099410 restraints weight = 16713.008| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.93 r_work: 0.3352 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1918 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= 0.151 Angle : 0.741 14.027 15028 Z= 0.336 Chirality : 0.048 0.547 1752 Planarity : 0.004 0.045 1802 Dihedral : 10.073 106.539 2154 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.33 % Favored : 94.51 % Rotamer: Outliers : 2.83 % Allowed : 28.00 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1256 helix: 1.73 (0.21), residues: 578 sheet: 0.92 (0.32), residues: 268 loop : -2.46 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.049 0.001 PHE B 705 TYR 0.035 0.001 TYR A 717 ARG 0.007 0.000 ARG B 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00960 ( 8) link_NAG-ASN : angle 7.06981 ( 24) link_BETA1-4 : bond 0.00375 ( 4) link_BETA1-4 : angle 3.41931 ( 12) hydrogen bonds : bond 0.04241 ( 612) hydrogen bonds : angle 4.24559 ( 1758) metal coordination : bond 0.00532 ( 6) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.57777 ( 12) covalent geometry : bond 0.00348 (10976) covalent geometry : angle 0.67887 (14980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5008.48 seconds wall clock time: 87 minutes 57.44 seconds (5277.44 seconds total)