Starting phenix.real_space_refine on Sun Jul 27 15:23:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6v_41082/07_2025/8t6v_41082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6v_41082/07_2025/8t6v_41082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6v_41082/07_2025/8t6v_41082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6v_41082/07_2025/8t6v_41082.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6v_41082/07_2025/8t6v_41082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6v_41082/07_2025/8t6v_41082.cif" } resolution = 2.95 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= 0.052 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 P 2 5.49 5 S 44 5.16 5 C 5832 2.51 5 N 1320 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8686 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 bond proxies already assigned to first conformer: 4169 Chain: "B" Number of atoms: 4082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 bond proxies already assigned to first conformer: 4169 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: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 147 Unusual residues: {'4DS': 1, 'CLR': 3, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 255 Unusual residues: {'4DS': 1, 'CLR': 3, 'PC1': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Time building chain proxies: 9.37, per 1000 atoms: 1.08 Number of scatterers: 8686 At special positions: 0 Unit cell: (87.723, 128.877, 85.557, 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) S 44 16.00 P 2 15.00 O 1488 8.00 N 1320 7.00 C 5832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 642 " " NAG D 1 " - " ASN B 642 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 2.0 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 74.4% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.735A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.856A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 516 Processing helix chain 'A' and resid 517 through 547 Processing helix chain 'A' and resid 569 through 593 Processing helix chain 'A' and resid 598 through 608 removed outlier: 3.502A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 667 through 690 removed outlier: 3.508A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 717 removed outlier: 3.517A pdb=" N ASP A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.517A pdb=" N LEU A 738 " --> pdb=" O HIS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 776 through 781 removed outlier: 3.555A pdb=" N LEU A 780 " --> pdb=" O MET A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 800 removed outlier: 3.730A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 800 " --> pdb=" O GLY A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.857A pdb=" N HIS A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 858 through 873 removed outlier: 3.671A pdb=" N LEU A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 866 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.828A pdb=" N ILE A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 removed outlier: 3.508A pdb=" N CYS A 885 " --> pdb=" O VAL A 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.734A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 485 through 507 removed outlier: 3.855A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 Processing helix chain 'B' and resid 517 through 547 Processing helix chain 'B' and resid 569 through 593 Processing helix chain 'B' and resid 598 through 608 removed outlier: 3.533A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 624 Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 667 through 690 removed outlier: 3.506A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 681 " --> pdb=" O LEU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 717 removed outlier: 3.515A pdb=" N ASP B 705 " --> pdb=" O GLY B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 720 No H-bonds generated for 'chain 'B' and resid 718 through 720' Processing helix chain 'B' and resid 727 through 738 removed outlier: 3.517A pdb=" N LEU B 738 " --> pdb=" O HIS B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 773 Processing helix chain 'B' and resid 776 through 781 removed outlier: 3.555A pdb=" N LEU B 780 " --> pdb=" O MET B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 800 removed outlier: 3.731A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 790 " --> pdb=" O ALA B 786 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 791 " --> pdb=" O VAL B 787 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 800 " --> pdb=" O GLY B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.856A pdb=" N HIS B 819 " --> pdb=" O PRO B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 858 through 873 removed outlier: 3.671A pdb=" N LEU B 865 " --> pdb=" O PHE B 861 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B 866 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 867 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Proline residue: B 868 - end of helix Processing helix chain 'B' and resid 873 through 878 removed outlier: 3.830A pdb=" N ILE B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 removed outlier: 3.509A pdb=" N CYS B 885 " --> pdb=" O VAL B 881 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742 removed outlier: 7.279A pdb=" N VAL A 740 " --> pdb=" O GLN A 754 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742 removed outlier: 7.279A pdb=" N VAL B 740 " --> pdb=" O GLN B 754 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1506 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: 2.60 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1236 1.30 - 1.44: 2316 1.44 - 1.57: 5226 1.57 - 1.71: 8 1.71 - 1.84: 70 Bond restraints: 8856 Sorted by residual: bond pdb=" CBA 4DS B2302 " pdb=" NAZ 4DS B2302 " ideal model delta sigma weight residual 1.170 1.303 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" CBA 4DS A2101 " pdb=" NAZ 4DS A2101 " ideal model delta sigma weight residual 1.170 1.299 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" CAT 4DS B2302 " pdb=" NAS 4DS B2302 " ideal model delta sigma weight residual 1.170 1.294 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" CAT 4DS A2101 " pdb=" NAS 4DS A2101 " ideal model delta sigma weight residual 1.170 1.294 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" OAY 4DS A2101 " pdb=" SAV 4DS A2101 " ideal model delta sigma weight residual 1.471 1.569 -0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 8851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.26: 12065 11.26 - 22.52: 1 22.52 - 33.77: 0 33.77 - 45.03: 2 45.03 - 56.29: 4 Bond angle restraints: 12072 Sorted by residual: angle pdb=" CAG 4DS B2302 " pdb=" NAZ 4DS B2302 " pdb=" CBA 4DS B2302 " ideal model delta sigma weight residual 177.62 121.33 56.29 3.00e+00 1.11e-01 3.52e+02 angle pdb=" CAG 4DS A2101 " pdb=" NAZ 4DS A2101 " pdb=" CBA 4DS A2101 " ideal model delta sigma weight residual 177.62 121.60 56.02 3.00e+00 1.11e-01 3.49e+02 angle pdb=" NAZ 4DS A2101 " pdb=" CBA 4DS A2101 " pdb=" SBB 4DS A2101 " ideal model delta sigma weight residual 180.00 125.06 54.94 3.00e+00 1.11e-01 3.35e+02 angle pdb=" NAZ 4DS B2302 " pdb=" CBA 4DS B2302 " pdb=" SBB 4DS B2302 " ideal model delta sigma weight residual 180.00 125.24 54.76 3.00e+00 1.11e-01 3.33e+02 angle pdb=" CAP 4DS B2302 " pdb=" NAS 4DS B2302 " pdb=" CAT 4DS B2302 " ideal model delta sigma weight residual 180.00 136.34 43.66 3.00e+00 1.11e-01 2.12e+02 ... (remaining 12067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 5134 16.87 - 33.74: 390 33.74 - 50.61: 84 50.61 - 67.49: 47 67.49 - 84.36: 13 Dihedral angle restraints: 5668 sinusoidal: 2684 harmonic: 2984 Sorted by residual: dihedral pdb=" CA GLN B 625 " pdb=" C GLN B 625 " pdb=" N ASP B 626 " pdb=" CA ASP B 626 " ideal model delta harmonic sigma weight residual -180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLN A 625 " pdb=" C GLN A 625 " pdb=" N ASP A 626 " pdb=" CA ASP A 626 " ideal model delta harmonic sigma weight residual 180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLN B 434 " pdb=" C GLN B 434 " pdb=" N MET B 435 " pdb=" CA MET B 435 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 736 0.057 - 0.114: 472 0.114 - 0.171: 158 0.171 - 0.227: 55 0.227 - 0.284: 17 Chirality restraints: 1438 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.22e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.37e+00 chirality pdb=" CB ILE A 877 " pdb=" CA ILE A 877 " pdb=" CG1 ILE A 877 " pdb=" CG2 ILE A 877 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1435 not shown) Planarity restraints: 1420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.330 2.00e-02 2.50e+03 2.80e-01 9.79e+02 pdb=" C7 NAG C 1 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.487 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.329 2.00e-02 2.50e+03 2.79e-01 9.75e+02 pdb=" C7 NAG D 1 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.486 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.209 2.00e-02 2.50e+03 1.73e-01 3.72e+02 pdb=" C7 NAG C 2 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.280 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.021 2.00e-02 2.50e+03 ... (remaining 1417 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2673 2.87 - 3.38: 8584 3.38 - 3.88: 14510 3.88 - 4.39: 17028 4.39 - 4.90: 28484 Nonbonded interactions: 71279 Sorted by model distance: nonbonded pdb=" OH TYR A 555 " pdb=" OH TYR B 555 " model vdw 2.358 3.040 nonbonded pdb=" ND1 HIS B 819 " pdb=" O HOH B2401 " model vdw 2.359 3.120 nonbonded pdb=" ND1 HIS A 819 " pdb=" O HOH A2201 " model vdw 2.361 3.120 nonbonded pdb=" O VAL A 634 " pdb=" O HOH A2202 " model vdw 2.388 3.040 nonbonded pdb=" O VAL B 634 " pdb=" O HOH B2402 " model vdw 2.394 3.040 ... (remaining 71274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 369 through 650 or resid 652 through 891 or resid 2105)) selection = (chain 'B' and (resid 369 through 650 or resid 652 through 891 or resid 2305)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.50 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: 0.910 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.730 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 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 : 0.012 0.133 8862 Z= 0.709 Angle : 1.863 56.288 12084 Z= 1.052 Chirality : 0.084 0.284 1438 Planarity : 0.017 0.280 1418 Dihedral : 14.216 84.357 3744 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.56 % Allowed : 4.67 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.70 (0.22), residues: 1026 helix: -1.44 (0.17), residues: 692 sheet: None (None), residues: 0 loop : -2.26 (0.29), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.008 TRP A 723 HIS 0.011 0.004 HIS B 547 PHE 0.042 0.010 PHE B 451 TYR 0.054 0.009 TYR A 534 ARG 0.019 0.003 ARG A 871 Details of bonding type rmsd link_NAG-ASN : bond 0.00880 ( 2) link_NAG-ASN : angle 4.65930 ( 6) link_BETA1-4 : bond 0.00468 ( 2) link_BETA1-4 : angle 0.77237 ( 6) hydrogen bonds : bond 0.24835 ( 520) hydrogen bonds : angle 7.88430 ( 1506) covalent geometry : bond 0.01171 ( 8856) covalent geometry : angle 1.86079 (12072) Misc. bond : bond 0.01583 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 MET cc_start: 0.9699 (tpt) cc_final: 0.9492 (mmm) REVERT: A 741 MET cc_start: 0.9680 (mmt) cc_final: 0.9326 (mmm) REVERT: A 752 GLN cc_start: 0.9608 (mm110) cc_final: 0.9060 (pp30) REVERT: A 882 GLU cc_start: 0.9603 (mt-10) cc_final: 0.9383 (mp0) REVERT: B 554 ASN cc_start: 0.9279 (m-40) cc_final: 0.8900 (t0) REVERT: B 559 MET cc_start: 0.9261 (mmm) cc_final: 0.8826 (mmm) REVERT: B 663 MET cc_start: 0.9696 (tpt) cc_final: 0.9487 (mmm) REVERT: B 741 MET cc_start: 0.9677 (mmt) cc_final: 0.9327 (mmm) REVERT: B 752 GLN cc_start: 0.9607 (mm110) cc_final: 0.9062 (pp30) REVERT: B 882 GLU cc_start: 0.9594 (mt-10) cc_final: 0.9379 (mp0) outliers start: 5 outliers final: 0 residues processed: 97 average time/residue: 1.2268 time to fit residues: 128.1054 Evaluate side-chains 56 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 92 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: A 433 ASN A 521 GLN A 545 GLN A 550 GLN B 433 ASN B 521 GLN B 545 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.053563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.042681 restraints weight = 83214.024| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 5.31 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8862 Z= 0.152 Angle : 0.677 11.819 12084 Z= 0.328 Chirality : 0.041 0.176 1438 Planarity : 0.006 0.045 1418 Dihedral : 9.499 80.766 1834 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.33 % Allowed : 8.11 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.25), residues: 1026 helix: 0.94 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.72 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 492 HIS 0.001 0.000 HIS A 703 PHE 0.012 0.001 PHE B 861 TYR 0.011 0.002 TYR B 519 ARG 0.008 0.001 ARG A 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 2) link_NAG-ASN : angle 1.41011 ( 6) link_BETA1-4 : bond 0.00499 ( 2) link_BETA1-4 : angle 1.26798 ( 6) hydrogen bonds : bond 0.06004 ( 520) hydrogen bonds : angle 4.70495 ( 1506) covalent geometry : bond 0.00328 ( 8856) covalent geometry : angle 0.67626 (12072) Misc. bond : bond 0.00079 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8776 (mt-10) REVERT: A 663 MET cc_start: 0.9830 (tpt) cc_final: 0.9573 (mmm) REVERT: A 741 MET cc_start: 0.9563 (mmt) cc_final: 0.9139 (mmm) REVERT: A 752 GLN cc_start: 0.9365 (mm110) cc_final: 0.8852 (pp30) REVERT: B 429 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8778 (mt-10) REVERT: B 554 ASN cc_start: 0.8659 (m-40) cc_final: 0.8422 (t0) REVERT: B 559 MET cc_start: 0.8898 (mmm) cc_final: 0.8427 (mmm) REVERT: B 663 MET cc_start: 0.9825 (tpt) cc_final: 0.9559 (mmm) REVERT: B 741 MET cc_start: 0.9555 (mmt) cc_final: 0.9137 (mmm) REVERT: B 752 GLN cc_start: 0.9383 (mm110) cc_final: 0.8853 (pp30) outliers start: 21 outliers final: 4 residues processed: 75 average time/residue: 2.0219 time to fit residues: 163.9773 Evaluate side-chains 60 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 593 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.052639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.042436 restraints weight = 62283.820| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 4.73 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8862 Z= 0.165 Angle : 0.619 8.996 12084 Z= 0.300 Chirality : 0.039 0.131 1438 Planarity : 0.006 0.059 1418 Dihedral : 9.095 89.120 1834 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.11 % Allowed : 8.78 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.26), residues: 1026 helix: 1.84 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.54 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 492 HIS 0.002 0.001 HIS B 547 PHE 0.012 0.001 PHE B 582 TYR 0.011 0.001 TYR A 824 ARG 0.010 0.001 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00029 ( 2) link_NAG-ASN : angle 2.11581 ( 6) link_BETA1-4 : bond 0.00417 ( 2) link_BETA1-4 : angle 1.00074 ( 6) hydrogen bonds : bond 0.05186 ( 520) hydrogen bonds : angle 4.41686 ( 1506) covalent geometry : bond 0.00387 ( 8856) covalent geometry : angle 0.61730 (12072) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8704 (mt-10) REVERT: A 663 MET cc_start: 0.9838 (tpt) cc_final: 0.9580 (tpp) REVERT: A 705 ASP cc_start: 0.9254 (m-30) cc_final: 0.8959 (m-30) REVERT: A 721 MET cc_start: 0.8961 (mtm) cc_final: 0.8614 (mmm) REVERT: B 429 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8681 (mt-10) REVERT: B 663 MET cc_start: 0.9841 (tpt) cc_final: 0.9581 (tpp) REVERT: B 705 ASP cc_start: 0.9267 (m-30) cc_final: 0.8971 (m-30) REVERT: B 721 MET cc_start: 0.8894 (mtm) cc_final: 0.8566 (mmm) outliers start: 10 outliers final: 4 residues processed: 62 average time/residue: 1.4914 time to fit residues: 99.7899 Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 73 optimal weight: 0.0070 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 0.0470 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 GLN B 593 ASN B 754 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.053903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.043464 restraints weight = 83487.360| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 5.46 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8862 Z= 0.116 Angle : 0.571 6.825 12084 Z= 0.275 Chirality : 0.038 0.138 1438 Planarity : 0.005 0.052 1418 Dihedral : 8.795 83.989 1834 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.33 % Allowed : 8.78 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.60 (0.27), residues: 1026 helix: 2.09 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.32 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 492 HIS 0.001 0.000 HIS A 547 PHE 0.010 0.001 PHE A 471 TYR 0.011 0.001 TYR A 519 ARG 0.011 0.001 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 2) link_NAG-ASN : angle 1.95595 ( 6) link_BETA1-4 : bond 0.00522 ( 2) link_BETA1-4 : angle 1.07169 ( 6) hydrogen bonds : bond 0.04620 ( 520) hydrogen bonds : angle 4.18356 ( 1506) covalent geometry : bond 0.00245 ( 8856) covalent geometry : angle 0.56915 (12072) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 1.055 Fit side-chains REVERT: A 429 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8768 (mt-10) REVERT: A 586 MET cc_start: 0.9437 (mmp) cc_final: 0.9052 (mmm) REVERT: A 663 MET cc_start: 0.9841 (tpt) cc_final: 0.9591 (tpp) REVERT: A 705 ASP cc_start: 0.9280 (m-30) cc_final: 0.9022 (m-30) REVERT: A 741 MET cc_start: 0.9571 (mmt) cc_final: 0.9154 (mmm) REVERT: B 429 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8766 (mt-10) REVERT: B 663 MET cc_start: 0.9844 (tpt) cc_final: 0.9589 (tpp) REVERT: B 705 ASP cc_start: 0.9296 (m-30) cc_final: 0.9024 (m-30) REVERT: B 741 MET cc_start: 0.9579 (mmt) cc_final: 0.9136 (mmm) outliers start: 12 outliers final: 2 residues processed: 66 average time/residue: 1.2984 time to fit residues: 92.6817 Evaluate side-chains 51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain B residue 418 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.053507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.043025 restraints weight = 89916.984| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 5.55 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8862 Z= 0.129 Angle : 0.577 6.812 12084 Z= 0.278 Chirality : 0.039 0.134 1438 Planarity : 0.005 0.055 1418 Dihedral : 8.650 81.050 1834 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.22 % Allowed : 10.11 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.71 (0.27), residues: 1026 helix: 2.16 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.24 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 492 HIS 0.002 0.000 HIS B 547 PHE 0.011 0.001 PHE A 471 TYR 0.011 0.001 TYR A 519 ARG 0.009 0.001 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00014 ( 2) link_NAG-ASN : angle 2.01148 ( 6) link_BETA1-4 : bond 0.00496 ( 2) link_BETA1-4 : angle 1.05167 ( 6) hydrogen bonds : bond 0.04549 ( 520) hydrogen bonds : angle 4.18019 ( 1506) covalent geometry : bond 0.00296 ( 8856) covalent geometry : angle 0.57498 (12072) Misc. bond : bond 0.00011 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.995 Fit side-chains REVERT: A 429 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8763 (mt-10) REVERT: A 586 MET cc_start: 0.9435 (mmp) cc_final: 0.9091 (mmm) REVERT: A 603 ARG cc_start: 0.8946 (mtp-110) cc_final: 0.8738 (mtm110) REVERT: A 663 MET cc_start: 0.9845 (tpt) cc_final: 0.9590 (tpp) REVERT: A 705 ASP cc_start: 0.9285 (m-30) cc_final: 0.9020 (m-30) REVERT: A 741 MET cc_start: 0.9580 (mmt) cc_final: 0.9182 (mmm) REVERT: B 429 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8765 (mt-10) REVERT: B 559 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.8918 (mmm) REVERT: B 663 MET cc_start: 0.9849 (tpt) cc_final: 0.9590 (tpp) REVERT: B 705 ASP cc_start: 0.9291 (m-30) cc_final: 0.9017 (m-30) REVERT: B 741 MET cc_start: 0.9596 (mmt) cc_final: 0.9200 (mmm) outliers start: 11 outliers final: 8 residues processed: 58 average time/residue: 1.2012 time to fit residues: 75.4594 Evaluate side-chains 58 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.053799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.043462 restraints weight = 71733.753| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 5.19 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8862 Z= 0.120 Angle : 0.589 9.756 12084 Z= 0.282 Chirality : 0.039 0.156 1438 Planarity : 0.005 0.065 1418 Dihedral : 8.539 78.137 1834 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.78 % Allowed : 8.67 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.27), residues: 1026 helix: 2.16 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 492 HIS 0.002 0.001 HIS A 547 PHE 0.011 0.001 PHE A 471 TYR 0.010 0.001 TYR B 519 ARG 0.014 0.001 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00005 ( 2) link_NAG-ASN : angle 2.02059 ( 6) link_BETA1-4 : bond 0.00442 ( 2) link_BETA1-4 : angle 1.05014 ( 6) hydrogen bonds : bond 0.04443 ( 520) hydrogen bonds : angle 4.11775 ( 1506) covalent geometry : bond 0.00267 ( 8856) covalent geometry : angle 0.58738 (12072) Misc. bond : bond 0.00003 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 1.711 Fit side-chains REVERT: A 429 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8756 (mt-10) REVERT: A 586 MET cc_start: 0.9446 (mmp) cc_final: 0.9085 (mmm) REVERT: A 603 ARG cc_start: 0.8940 (mtp-110) cc_final: 0.8628 (ptm160) REVERT: A 663 MET cc_start: 0.9837 (tpt) cc_final: 0.9576 (tpp) REVERT: A 705 ASP cc_start: 0.9265 (m-30) cc_final: 0.9007 (m-30) REVERT: A 741 MET cc_start: 0.9581 (mmt) cc_final: 0.9184 (mmm) REVERT: B 429 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8762 (mt-10) REVERT: B 559 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.8886 (mmm) REVERT: B 663 MET cc_start: 0.9841 (tpt) cc_final: 0.9575 (tpp) REVERT: B 705 ASP cc_start: 0.9272 (m-30) cc_final: 0.9006 (m-30) REVERT: B 741 MET cc_start: 0.9598 (mmt) cc_final: 0.9213 (mmm) outliers start: 16 outliers final: 5 residues processed: 61 average time/residue: 1.4604 time to fit residues: 96.8710 Evaluate side-chains 55 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 664 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.053632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.043266 restraints weight = 77777.902| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 5.34 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8862 Z= 0.126 Angle : 0.586 10.975 12084 Z= 0.280 Chirality : 0.039 0.183 1438 Planarity : 0.005 0.045 1418 Dihedral : 8.430 75.410 1834 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.67 % Allowed : 8.56 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.27), residues: 1026 helix: 2.17 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.15 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 492 HIS 0.002 0.000 HIS B 547 PHE 0.011 0.001 PHE A 471 TYR 0.010 0.001 TYR B 519 ARG 0.009 0.001 ARG A 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00026 ( 2) link_NAG-ASN : angle 2.02537 ( 6) link_BETA1-4 : bond 0.00447 ( 2) link_BETA1-4 : angle 1.05412 ( 6) hydrogen bonds : bond 0.04386 ( 520) hydrogen bonds : angle 4.10799 ( 1506) covalent geometry : bond 0.00290 ( 8856) covalent geometry : angle 0.58448 (12072) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 1.297 Fit side-chains REVERT: A 429 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8770 (mt-10) REVERT: A 543 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9304 (tp) REVERT: A 586 MET cc_start: 0.9423 (mmp) cc_final: 0.9093 (mmm) REVERT: A 663 MET cc_start: 0.9843 (tpt) cc_final: 0.9579 (tpp) REVERT: A 705 ASP cc_start: 0.9263 (m-30) cc_final: 0.9009 (m-30) REVERT: A 741 MET cc_start: 0.9576 (mmt) cc_final: 0.9187 (mmm) REVERT: B 429 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8771 (mt-10) REVERT: B 559 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8832 (mmm) REVERT: B 663 MET cc_start: 0.9847 (tpt) cc_final: 0.9586 (tpp) REVERT: B 705 ASP cc_start: 0.9277 (m-30) cc_final: 0.9015 (m-30) REVERT: B 741 MET cc_start: 0.9598 (mmt) cc_final: 0.9208 (mmm) outliers start: 15 outliers final: 7 residues processed: 58 average time/residue: 1.3723 time to fit residues: 86.3201 Evaluate side-chains 56 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 25 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.2890 r_free = 0.2890 target = 0.054069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.043608 restraints weight = 88184.737| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 5.58 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8862 Z= 0.115 Angle : 0.579 10.721 12084 Z= 0.278 Chirality : 0.039 0.206 1438 Planarity : 0.005 0.084 1418 Dihedral : 8.312 71.821 1834 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.33 % Allowed : 8.89 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.27), residues: 1026 helix: 2.18 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.12 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 492 HIS 0.002 0.000 HIS A 547 PHE 0.011 0.001 PHE A 471 TYR 0.010 0.001 TYR A 519 ARG 0.014 0.001 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00017 ( 2) link_NAG-ASN : angle 2.01145 ( 6) link_BETA1-4 : bond 0.00517 ( 2) link_BETA1-4 : angle 1.09047 ( 6) hydrogen bonds : bond 0.04262 ( 520) hydrogen bonds : angle 4.04275 ( 1506) covalent geometry : bond 0.00253 ( 8856) covalent geometry : angle 0.57706 (12072) Misc. bond : bond 0.00044 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.977 Fit side-chains REVERT: A 429 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8719 (mt-10) REVERT: A 586 MET cc_start: 0.9426 (mmp) cc_final: 0.9142 (mmm) REVERT: A 663 MET cc_start: 0.9840 (tpt) cc_final: 0.9569 (tpp) REVERT: A 705 ASP cc_start: 0.9263 (m-30) cc_final: 0.9026 (m-30) REVERT: A 741 MET cc_start: 0.9586 (mmt) cc_final: 0.9189 (mmm) REVERT: B 429 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8723 (mt-10) REVERT: B 559 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8813 (mmm) REVERT: B 586 MET cc_start: 0.9488 (mmp) cc_final: 0.9168 (mmm) REVERT: B 603 ARG cc_start: 0.8908 (mtp-110) cc_final: 0.8678 (mtm-85) REVERT: B 663 MET cc_start: 0.9842 (tpt) cc_final: 0.9569 (tpp) REVERT: B 705 ASP cc_start: 0.9287 (m-30) cc_final: 0.9043 (m-30) REVERT: B 741 MET cc_start: 0.9594 (mmt) cc_final: 0.9213 (mmm) outliers start: 12 outliers final: 5 residues processed: 54 average time/residue: 1.1300 time to fit residues: 66.3126 Evaluate side-chains 54 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.2884 r_free = 0.2884 target = 0.053877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.043615 restraints weight = 77111.429| |-----------------------------------------------------------------------------| r_work (start): 0.2583 rms_B_bonded: 5.26 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8862 Z= 0.120 Angle : 0.582 12.309 12084 Z= 0.277 Chirality : 0.038 0.205 1438 Planarity : 0.005 0.059 1418 Dihedral : 8.267 70.307 1834 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.89 % Allowed : 9.56 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.27), residues: 1026 helix: 2.21 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.12 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 492 HIS 0.002 0.000 HIS A 547 PHE 0.011 0.001 PHE A 471 TYR 0.010 0.001 TYR B 519 ARG 0.013 0.001 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00009 ( 2) link_NAG-ASN : angle 2.00177 ( 6) link_BETA1-4 : bond 0.00454 ( 2) link_BETA1-4 : angle 1.04810 ( 6) hydrogen bonds : bond 0.04266 ( 520) hydrogen bonds : angle 4.04849 ( 1506) covalent geometry : bond 0.00275 ( 8856) covalent geometry : angle 0.57971 (12072) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.188 Fit side-chains REVERT: A 429 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8716 (mt-10) REVERT: A 586 MET cc_start: 0.9453 (mmp) cc_final: 0.9155 (mmm) REVERT: A 663 MET cc_start: 0.9840 (tpt) cc_final: 0.9570 (tpp) REVERT: A 664 MET cc_start: 0.9580 (ttp) cc_final: 0.9242 (tpp) REVERT: A 705 ASP cc_start: 0.9247 (m-30) cc_final: 0.9003 (m-30) REVERT: A 741 MET cc_start: 0.9575 (mmt) cc_final: 0.9158 (mmm) REVERT: B 429 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8719 (mt-10) REVERT: B 559 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8800 (mmm) REVERT: B 586 MET cc_start: 0.9471 (mmp) cc_final: 0.9184 (mmm) REVERT: B 603 ARG cc_start: 0.8903 (mtp-110) cc_final: 0.8660 (mtm-85) REVERT: B 663 MET cc_start: 0.9840 (tpt) cc_final: 0.9600 (tpp) REVERT: B 705 ASP cc_start: 0.9270 (m-30) cc_final: 0.9019 (m-30) REVERT: B 741 MET cc_start: 0.9591 (mmt) cc_final: 0.9216 (mmm) outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 1.4058 time to fit residues: 82.5879 Evaluate side-chains 54 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 19 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.2893 r_free = 0.2893 target = 0.054353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.044152 restraints weight = 73584.191| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 5.21 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 8862 Z= 0.112 Angle : 0.583 12.458 12084 Z= 0.277 Chirality : 0.038 0.210 1438 Planarity : 0.005 0.058 1418 Dihedral : 8.170 68.081 1834 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.89 % Allowed : 9.56 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.77 (0.27), residues: 1026 helix: 2.19 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 492 HIS 0.002 0.000 HIS B 834 PHE 0.011 0.001 PHE A 471 TYR 0.009 0.001 TYR B 824 ARG 0.013 0.001 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00030 ( 2) link_NAG-ASN : angle 1.99072 ( 6) link_BETA1-4 : bond 0.00469 ( 2) link_BETA1-4 : angle 1.06631 ( 6) hydrogen bonds : bond 0.04213 ( 520) hydrogen bonds : angle 4.02095 ( 1506) covalent geometry : bond 0.00243 ( 8856) covalent geometry : angle 0.58113 (12072) Misc. bond : bond 0.00050 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.930 Fit side-chains REVERT: A 429 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8724 (mt-10) REVERT: A 586 MET cc_start: 0.9437 (mmp) cc_final: 0.9118 (mmm) REVERT: A 663 MET cc_start: 0.9837 (tpt) cc_final: 0.9603 (tpp) REVERT: A 664 MET cc_start: 0.9587 (ttp) cc_final: 0.9132 (tpp) REVERT: A 705 ASP cc_start: 0.9241 (m-30) cc_final: 0.9000 (m-30) REVERT: A 741 MET cc_start: 0.9574 (mmt) cc_final: 0.9154 (mmm) REVERT: B 429 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8730 (mt-10) REVERT: B 586 MET cc_start: 0.9463 (mmp) cc_final: 0.9130 (mmm) REVERT: B 603 ARG cc_start: 0.8907 (mtp-110) cc_final: 0.8675 (mtm-85) REVERT: B 663 MET cc_start: 0.9838 (tpt) cc_final: 0.9602 (tpp) REVERT: B 664 MET cc_start: 0.9581 (ttp) cc_final: 0.9242 (tpp) REVERT: B 705 ASP cc_start: 0.9263 (m-30) cc_final: 0.9015 (m-30) REVERT: B 741 MET cc_start: 0.9591 (mmt) cc_final: 0.9214 (mmm) outliers start: 8 outliers final: 4 residues processed: 56 average time/residue: 1.1630 time to fit residues: 70.6021 Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.2877 r_free = 0.2877 target = 0.053533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.043243 restraints weight = 87842.058| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 5.45 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 8862 Z= 0.148 Angle : 0.591 11.579 12084 Z= 0.282 Chirality : 0.039 0.215 1438 Planarity : 0.005 0.056 1418 Dihedral : 8.055 66.279 1834 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.67 % Allowed : 9.89 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.27), residues: 1026 helix: 2.25 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.10 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 492 HIS 0.004 0.001 HIS B 834 PHE 0.011 0.001 PHE A 471 TYR 0.011 0.001 TYR B 519 ARG 0.013 0.001 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 2) link_NAG-ASN : angle 2.04607 ( 6) link_BETA1-4 : bond 0.00449 ( 2) link_BETA1-4 : angle 1.03784 ( 6) hydrogen bonds : bond 0.04239 ( 520) hydrogen bonds : angle 4.08632 ( 1506) covalent geometry : bond 0.00353 ( 8856) covalent geometry : angle 0.58868 (12072) Misc. bond : bond 0.00006 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5419.50 seconds wall clock time: 97 minutes 31.65 seconds (5851.65 seconds total)