Starting phenix.real_space_refine on Thu Jul 2 17:25:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t6v_41082/07_2026/8t6v_41082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6v_41082/07_2026/8t6v_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8t6v_41082/07_2026/8t6v_41082.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t6v_41082/07_2026/8t6v_41082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t6v_41082/07_2026/8t6v_41082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6v_41082/07_2026/8t6v_41082.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6v_41082/07_2026/8t6v_41082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6v_41082/07_2026/8t6v_41082.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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: 2.42, per 1000 atoms: 0.28 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: 0.65 Conformation dependent library (CDL) restraints added in 356.9 milliseconds 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: 0.14 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: 1.00 Time building geometry restraints manager: 0.82 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: 4622 16.87 - 33.74: 360 33.74 - 50.61: 76 50.61 - 67.49: 43 67.49 - 84.36: 13 Dihedral angle restraints: 5114 sinusoidal: 2130 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 5111 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: 1.500 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.120 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 : 14.804 84.357 3190 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.019 0.003 ARG A 871 TYR 0.054 0.009 TYR A 534 PHE 0.042 0.010 PHE B 451 TRP 0.031 0.008 TRP A 723 HIS 0.011 0.004 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.01171 / 0.71 ( 8856) covalent geometry : angle 1.86079 / 1.05 (12072) hydrogen bonds : bond 0.24835 / 16.22 ( 520) hydrogen bonds : angle 7.88430 / 5.66 ( 1506) Misc. bond : bond 0.01583 / 0.80 ( 2) link_BETA1-4 : bond 0.00468 / 0.24 ( 2) link_BETA1-4 : angle 0.77237 / 0.63 ( 6) link_NAG-ASN : bond 0.00880 / 0.44 ( 2) link_NAG-ASN : angle 4.65930 / 2.62 ( 6) *********************** 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 : 0.324 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: 0.4518 time to fit residues: 46.9010 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 : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2880 r_free = 0.2880 target = 0.053677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.043050 restraints weight = 68693.034| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 4.95 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 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 = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1819 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= 0.154 Angle : 0.676 12.062 12084 Z= 0.328 Chirality : 0.041 0.152 1438 Planarity : 0.006 0.046 1418 Dihedral : 10.581 80.248 1280 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.33 % Allowed : 8.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1026 helix: 0.93 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.73 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 603 TYR 0.011 0.002 TYR B 519 PHE 0.012 0.001 PHE B 861 TRP 0.021 0.002 TRP A 492 HIS 0.001 0.000 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 8856) covalent geometry : angle 0.67481 / 0.33 (12072) hydrogen bonds : bond 0.05969 / 3.89 ( 520) hydrogen bonds : angle 4.70513 / 3.41 ( 1506) Misc. bond : bond 0.00036 / 0.02 ( 2) link_BETA1-4 : bond 0.00243 / 0.13 ( 2) link_BETA1-4 : angle 1.35595 / 0.81 ( 6) link_NAG-ASN : bond 0.00142 / 0.07 ( 2) link_NAG-ASN : angle 1.35562 / 0.71 ( 6) *********************** 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 81 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8784 (mt-10) REVERT: A 663 MET cc_start: 0.9826 (tpt) cc_final: 0.9565 (mmm) REVERT: A 741 MET cc_start: 0.9556 (mmt) cc_final: 0.9140 (mmm) REVERT: A 752 GLN cc_start: 0.9348 (mm110) cc_final: 0.8858 (pp30) REVERT: B 429 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8781 (mt-10) REVERT: B 554 ASN cc_start: 0.8655 (m-40) cc_final: 0.8433 (t0) REVERT: B 559 MET cc_start: 0.8904 (mmm) cc_final: 0.8435 (mmm) REVERT: B 663 MET cc_start: 0.9817 (tpt) cc_final: 0.9547 (mmm) REVERT: B 741 MET cc_start: 0.9550 (mmt) cc_final: 0.9133 (mmm) REVERT: B 752 GLN cc_start: 0.9368 (mm110) cc_final: 0.8852 (pp30) outliers start: 21 outliers final: 4 residues processed: 76 average time/residue: 0.4468 time to fit residues: 36.4342 Evaluate side-chains 59 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2881 r_free = 0.2881 target = 0.053989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.043336 restraints weight = 90610.217| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 5.49 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 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 = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8862 Z= 0.129 Angle : 0.601 9.151 12084 Z= 0.293 Chirality : 0.039 0.147 1438 Planarity : 0.006 0.062 1418 Dihedral : 9.633 82.759 1280 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.11 % Allowed : 9.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1026 helix: 1.74 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -1.54 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 603 TYR 0.012 0.001 TYR B 519 PHE 0.012 0.001 PHE B 582 TRP 0.015 0.001 TRP B 492 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8856) covalent geometry : angle 0.59957 / 0.29 (12072) hydrogen bonds : bond 0.05037 / 3.28 ( 520) hydrogen bonds : angle 4.38382 / 3.19 ( 1506) Misc. bond : bond 0.00023 / 0.01 ( 2) link_BETA1-4 : bond 0.00326 / 0.17 ( 2) link_BETA1-4 : angle 1.26407 / 0.72 ( 6) link_NAG-ASN : bond 0.00023 / 0.01 ( 2) link_NAG-ASN : angle 1.88787 / 1.14 ( 6) *********************** 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 66 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 429 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8732 (mt-10) REVERT: A 663 MET cc_start: 0.9836 (tpt) cc_final: 0.9591 (tpp) REVERT: A 721 MET cc_start: 0.8869 (mtm) cc_final: 0.8562 (mmm) REVERT: A 741 MET cc_start: 0.9563 (mmt) cc_final: 0.9088 (mmm) REVERT: A 752 GLN cc_start: 0.9379 (mm110) cc_final: 0.8831 (pp30) REVERT: B 429 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8732 (mt-10) REVERT: B 554 ASN cc_start: 0.8679 (m-40) cc_final: 0.8456 (t0) REVERT: B 559 MET cc_start: 0.8949 (mmm) cc_final: 0.8471 (mmm) REVERT: B 663 MET cc_start: 0.9834 (tpt) cc_final: 0.9582 (tpp) REVERT: B 705 ASP cc_start: 0.9296 (m-30) cc_final: 0.9010 (m-30) REVERT: B 741 MET cc_start: 0.9557 (mmt) cc_final: 0.9083 (mmm) REVERT: B 752 GLN cc_start: 0.9390 (mm110) cc_final: 0.8836 (pp30) outliers start: 10 outliers final: 2 residues processed: 66 average time/residue: 0.4831 time to fit residues: 34.1665 Evaluate side-chains 55 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain B residue 418 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 593 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.053740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.043111 restraints weight = 90170.626| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 5.51 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 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 = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2340 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= 0.133 Angle : 0.585 7.405 12084 Z= 0.284 Chirality : 0.039 0.126 1438 Planarity : 0.005 0.053 1418 Dihedral : 9.129 86.575 1280 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.44 % Allowed : 9.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.27), residues: 1026 helix: 2.08 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.31 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 603 TYR 0.011 0.001 TYR A 519 PHE 0.011 0.001 PHE B 861 TRP 0.017 0.001 TRP B 492 HIS 0.002 0.000 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8856) covalent geometry : angle 0.58336 / 0.28 (12072) hydrogen bonds : bond 0.04695 / 3.05 ( 520) hydrogen bonds : angle 4.25343 / 3.09 ( 1506) Misc. bond : bond 0.00097 / 0.05 ( 2) link_BETA1-4 : bond 0.00393 / 0.20 ( 2) link_BETA1-4 : angle 1.02432 / 0.53 ( 6) link_NAG-ASN : bond 0.00011 / 0.01 ( 2) link_NAG-ASN : angle 1.87512 / 1.12 ( 6) *********************** 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 63 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.332 Fit side-chains REVERT: A 429 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8754 (mt-10) REVERT: A 663 MET cc_start: 0.9842 (tpt) cc_final: 0.9589 (tpp) REVERT: A 705 ASP cc_start: 0.9292 (m-30) cc_final: 0.9027 (m-30) REVERT: A 741 MET cc_start: 0.9552 (mmt) cc_final: 0.9016 (mmm) REVERT: B 429 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8774 (mt-10) REVERT: B 663 MET cc_start: 0.9843 (tpt) cc_final: 0.9588 (tpp) REVERT: B 705 ASP cc_start: 0.9291 (m-30) cc_final: 0.9023 (m-30) REVERT: B 741 MET cc_start: 0.9545 (mmt) cc_final: 0.8996 (mmm) outliers start: 13 outliers final: 5 residues processed: 62 average time/residue: 0.5008 time to fit residues: 33.3694 Evaluate side-chains 51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 543 ILE Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 593 ASN A 754 GLN B 593 ASN B 754 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.053537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.043165 restraints weight = 74513.507| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 5.23 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8862 Z= 0.131 Angle : 0.572 6.671 12084 Z= 0.274 Chirality : 0.038 0.124 1438 Planarity : 0.005 0.055 1418 Dihedral : 8.909 87.916 1280 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.44 % Allowed : 9.33 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.27), residues: 1026 helix: 2.20 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.17 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 603 TYR 0.011 0.001 TYR A 824 PHE 0.011 0.001 PHE A 471 TRP 0.016 0.001 TRP B 492 HIS 0.002 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8856) covalent geometry : angle 0.56984 / 0.27 (12072) hydrogen bonds : bond 0.04523 / 2.95 ( 520) hydrogen bonds : angle 4.15038 / 3.02 ( 1506) Misc. bond : bond 0.00028 / 0.01 ( 2) link_BETA1-4 : bond 0.00467 / 0.24 ( 2) link_BETA1-4 : angle 1.05374 / 0.55 ( 6) link_NAG-ASN : bond 0.00042 / 0.02 ( 2) link_NAG-ASN : angle 1.87384 / 1.11 ( 6) *********************** 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 59 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.187 Fit side-chains REVERT: A 429 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8768 (mt-10) REVERT: A 603 ARG cc_start: 0.8938 (mtp-110) cc_final: 0.8737 (mtm110) REVERT: A 663 MET cc_start: 0.9841 (tpt) cc_final: 0.9578 (tpp) REVERT: A 705 ASP cc_start: 0.9288 (m-30) cc_final: 0.9034 (m-30) REVERT: A 741 MET cc_start: 0.9534 (mmt) cc_final: 0.9140 (mmm) REVERT: B 429 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8776 (mt-10) REVERT: B 586 MET cc_start: 0.9463 (mmp) cc_final: 0.9190 (mmm) REVERT: B 663 MET cc_start: 0.9844 (tpt) cc_final: 0.9575 (tpp) REVERT: B 705 ASP cc_start: 0.9291 (m-30) cc_final: 0.9029 (m-30) REVERT: B 741 MET cc_start: 0.9537 (mmt) cc_final: 0.9147 (mmm) outliers start: 13 outliers final: 7 residues processed: 57 average time/residue: 0.4639 time to fit residues: 28.4471 Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER 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 530 LEU 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 94 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 593 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.053697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.043580 restraints weight = 63127.623| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 4.89 r_work (final): 0.2576 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8862 Z= 0.122 Angle : 0.571 8.938 12084 Z= 0.273 Chirality : 0.038 0.139 1438 Planarity : 0.005 0.060 1418 Dihedral : 8.739 85.254 1280 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.22 % Allowed : 9.11 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.27), residues: 1026 helix: 2.25 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.16 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 603 TYR 0.010 0.001 TYR B 519 PHE 0.011 0.001 PHE A 471 TRP 0.016 0.001 TRP A 492 HIS 0.002 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 8856) covalent geometry : angle 0.56951 / 0.27 (12072) hydrogen bonds : bond 0.04427 / 2.88 ( 520) hydrogen bonds : angle 4.11097 / 2.99 ( 1506) Misc. bond : bond 0.00024 / 0.01 ( 2) link_BETA1-4 : bond 0.00496 / 0.25 ( 2) link_BETA1-4 : angle 1.04919 / 0.54 ( 6) link_NAG-ASN : bond 0.00036 / 0.02 ( 2) link_NAG-ASN : angle 1.86031 / 1.09 ( 6) *********************** 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 59 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.326 Fit side-chains REVERT: A 429 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8757 (mt-10) REVERT: A 663 MET cc_start: 0.9837 (tpt) cc_final: 0.9570 (tpp) REVERT: A 705 ASP cc_start: 0.9247 (m-30) cc_final: 0.8987 (m-30) REVERT: A 741 MET cc_start: 0.9577 (mmt) cc_final: 0.9216 (mmm) REVERT: B 429 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8757 (mt-10) REVERT: B 586 MET cc_start: 0.9474 (mmp) cc_final: 0.9171 (mmm) REVERT: B 663 MET cc_start: 0.9844 (tpt) cc_final: 0.9570 (tpp) REVERT: B 705 ASP cc_start: 0.9254 (m-30) cc_final: 0.8984 (m-30) REVERT: B 741 MET cc_start: 0.9576 (mmt) cc_final: 0.9213 (mmm) outliers start: 11 outliers final: 7 residues processed: 59 average time/residue: 0.4239 time to fit residues: 27.1693 Evaluate side-chains 53 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER 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 530 LEU Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.0020 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.053953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.043983 restraints weight = 55953.552| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 4.60 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2795 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= 0.116 Angle : 0.580 11.273 12084 Z= 0.276 Chirality : 0.038 0.169 1438 Planarity : 0.005 0.067 1418 Dihedral : 8.605 82.798 1280 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.22 % Allowed : 9.56 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.27), residues: 1026 helix: 2.22 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.15 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 603 TYR 0.010 0.001 TYR A 824 PHE 0.011 0.001 PHE A 471 TRP 0.016 0.001 TRP A 492 HIS 0.002 0.000 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 8856) covalent geometry : angle 0.57810 / 0.28 (12072) hydrogen bonds : bond 0.04310 / 2.80 ( 520) hydrogen bonds : angle 4.05508 / 2.95 ( 1506) Misc. bond : bond 0.00050 / 0.03 ( 2) link_BETA1-4 : bond 0.00425 / 0.21 ( 2) link_BETA1-4 : angle 1.01529 / 0.52 ( 6) link_NAG-ASN : bond 0.00017 / 0.01 ( 2) link_NAG-ASN : angle 1.83205 / 1.06 ( 6) *********************** 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 59 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.274 Fit side-chains REVERT: A 429 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8705 (mt-10) REVERT: A 586 MET cc_start: 0.9473 (mmp) cc_final: 0.9172 (mmm) REVERT: A 663 MET cc_start: 0.9836 (tpt) cc_final: 0.9558 (tpp) REVERT: A 705 ASP cc_start: 0.9222 (m-30) cc_final: 0.8957 (m-30) REVERT: A 741 MET cc_start: 0.9584 (mmt) cc_final: 0.9206 (mmm) REVERT: B 429 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8705 (mt-10) REVERT: B 586 MET cc_start: 0.9489 (mmp) cc_final: 0.9227 (mmm) REVERT: B 663 MET cc_start: 0.9837 (tpt) cc_final: 0.9553 (tpp) REVERT: B 705 ASP cc_start: 0.9237 (m-30) cc_final: 0.8971 (m-30) REVERT: B 741 MET cc_start: 0.9581 (mmt) cc_final: 0.9205 (mmm) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 0.4712 time to fit residues: 27.8889 Evaluate side-chains 53 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 530 LEU 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 22 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 593 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.053628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.043300 restraints weight = 81189.517| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 5.31 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 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 = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2910 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= 0.124 Angle : 0.570 12.070 12084 Z= 0.274 Chirality : 0.038 0.178 1438 Planarity : 0.005 0.079 1418 Dihedral : 8.443 79.324 1280 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.22 % Allowed : 9.56 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.27), residues: 1026 helix: 2.25 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.08 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 603 TYR 0.010 0.001 TYR A 824 PHE 0.011 0.001 PHE A 471 TRP 0.018 0.001 TRP A 492 HIS 0.002 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8856) covalent geometry : angle 0.56819 / 0.27 (12072) hydrogen bonds : bond 0.04298 / 2.78 ( 520) hydrogen bonds : angle 4.03993 / 2.94 ( 1506) Misc. bond : bond 0.00009 / 0.00 ( 2) link_BETA1-4 : bond 0.00373 / 0.19 ( 2) link_BETA1-4 : angle 0.97285 / 0.50 ( 6) link_NAG-ASN : bond 0.00048 / 0.02 ( 2) link_NAG-ASN : angle 1.85245 / 1.08 ( 6) *********************** 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 58 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.234 Fit side-chains REVERT: A 429 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8711 (mt-10) REVERT: A 586 MET cc_start: 0.9443 (mmp) cc_final: 0.9129 (mmm) REVERT: A 663 MET cc_start: 0.9840 (tpt) cc_final: 0.9600 (tpp) REVERT: A 664 MET cc_start: 0.9601 (ttp) cc_final: 0.9162 (tpp) REVERT: A 705 ASP cc_start: 0.9291 (m-30) cc_final: 0.9032 (m-30) REVERT: A 741 MET cc_start: 0.9588 (mmt) cc_final: 0.9198 (mmm) REVERT: B 429 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8712 (mt-10) REVERT: B 586 MET cc_start: 0.9463 (mmp) cc_final: 0.9223 (mmm) REVERT: B 603 ARG cc_start: 0.8899 (mtp-110) cc_final: 0.8662 (mtm-85) REVERT: B 663 MET cc_start: 0.9839 (tpt) cc_final: 0.9596 (tpp) REVERT: B 664 MET cc_start: 0.9600 (ttp) cc_final: 0.9301 (tpp) REVERT: B 705 ASP cc_start: 0.9278 (m-30) cc_final: 0.9032 (m-30) REVERT: B 721 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8396 (mmm) REVERT: B 741 MET cc_start: 0.9592 (mmt) cc_final: 0.9207 (mmm) outliers start: 11 outliers final: 4 residues processed: 53 average time/residue: 0.4963 time to fit residues: 28.2079 Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 721 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 38 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 0.0040 chunk 37 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.053714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.043199 restraints weight = 102156.583| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 5.75 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 8862 Z= 0.127 Angle : 0.590 12.777 12084 Z= 0.279 Chirality : 0.038 0.210 1438 Planarity : 0.005 0.063 1418 Dihedral : 8.390 78.324 1280 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.00 % Allowed : 9.78 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.27), residues: 1026 helix: 2.25 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.06 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 603 TYR 0.010 0.001 TYR A 824 PHE 0.011 0.001 PHE A 471 TRP 0.016 0.001 TRP A 492 HIS 0.002 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8856) covalent geometry : angle 0.58863 / 0.28 (12072) hydrogen bonds : bond 0.04287 / 2.78 ( 520) hydrogen bonds : angle 4.05712 / 2.96 ( 1506) Misc. bond : bond 0.00006 / 0.00 ( 2) link_BETA1-4 : bond 0.00383 / 0.19 ( 2) link_BETA1-4 : angle 0.97368 / 0.50 ( 6) link_NAG-ASN : bond 0.00039 / 0.02 ( 2) link_NAG-ASN : angle 1.83754 / 1.07 ( 6) *********************** 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: 9 poor density : 47 time to evaluate : 0.292 Fit side-chains REVERT: A 429 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8773 (mt-10) REVERT: A 586 MET cc_start: 0.9429 (mmp) cc_final: 0.9124 (mmm) REVERT: A 603 ARG cc_start: 0.8936 (mtp-110) cc_final: 0.8593 (mtm-85) REVERT: A 663 MET cc_start: 0.9826 (tpt) cc_final: 0.9586 (tpp) REVERT: A 664 MET cc_start: 0.9597 (ttp) cc_final: 0.9282 (tpp) REVERT: A 705 ASP cc_start: 0.9307 (m-30) cc_final: 0.9057 (m-30) REVERT: A 741 MET cc_start: 0.9599 (mmt) cc_final: 0.9207 (mmm) REVERT: B 429 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8721 (mt-10) REVERT: B 586 MET cc_start: 0.9441 (mmp) cc_final: 0.9156 (mmm) REVERT: B 603 ARG cc_start: 0.8915 (mtp-110) cc_final: 0.8679 (mtm-85) REVERT: B 663 MET cc_start: 0.9836 (tpt) cc_final: 0.9593 (tpp) REVERT: B 664 MET cc_start: 0.9595 (ttp) cc_final: 0.9275 (tpp) REVERT: B 705 ASP cc_start: 0.9291 (m-30) cc_final: 0.9051 (m-30) REVERT: B 741 MET cc_start: 0.9598 (mmt) cc_final: 0.9214 (mmm) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 0.4921 time to fit residues: 29.1554 Evaluate side-chains 51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 78 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 91 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.053547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.043424 restraints weight = 73414.546| |-----------------------------------------------------------------------------| r_work (start): 0.2584 rms_B_bonded: 5.11 r_work (final): 0.2584 ------------------------------------------------------------------------------- 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 = 0.43 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 = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2969 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= 0.131 Angle : 0.593 12.762 12084 Z= 0.281 Chirality : 0.038 0.214 1438 Planarity : 0.005 0.061 1418 Dihedral : 8.351 77.514 1280 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.44 % Allowed : 10.33 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.27), residues: 1026 helix: 2.26 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.04 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 603 TYR 0.010 0.001 TYR A 824 PHE 0.011 0.001 PHE A 471 TRP 0.016 0.001 TRP A 492 HIS 0.002 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8856) covalent geometry : angle 0.59124 / 0.28 (12072) hydrogen bonds : bond 0.04279 / 2.77 ( 520) hydrogen bonds : angle 4.06332 / 2.96 ( 1506) Misc. bond : bond 0.00005 / 0.00 ( 2) link_BETA1-4 : bond 0.00375 / 0.19 ( 2) link_BETA1-4 : angle 0.96880 / 0.50 ( 6) link_NAG-ASN : bond 0.00047 / 0.02 ( 2) link_NAG-ASN : angle 1.83828 / 1.07 ( 6) ********************** 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 51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.368 Fit side-chains REVERT: A 429 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8760 (mt-10) REVERT: A 586 MET cc_start: 0.9441 (mmp) cc_final: 0.9137 (mmm) REVERT: A 603 ARG cc_start: 0.8923 (mtp-110) cc_final: 0.8575 (mtm-85) REVERT: A 663 MET cc_start: 0.9821 (tpt) cc_final: 0.9576 (tpp) REVERT: A 705 ASP cc_start: 0.9284 (m-30) cc_final: 0.9025 (m-30) REVERT: A 741 MET cc_start: 0.9592 (mmt) cc_final: 0.9218 (mmm) REVERT: B 429 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8709 (mt-10) REVERT: B 586 MET cc_start: 0.9462 (mmp) cc_final: 0.9173 (mmm) REVERT: B 603 ARG cc_start: 0.8903 (mtp-110) cc_final: 0.8668 (mtm-85) REVERT: B 663 MET cc_start: 0.9821 (tpt) cc_final: 0.9572 (tpp) REVERT: B 705 ASP cc_start: 0.9263 (m-30) cc_final: 0.9010 (m-30) REVERT: B 741 MET cc_start: 0.9593 (mmt) cc_final: 0.9225 (mmm) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.5097 time to fit residues: 27.9249 Evaluate side-chains 49 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 873 LEU 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 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 chunk 10 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 0.0060 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.3170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.054222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.043920 restraints weight = 83108.644| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 5.40 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 8862 Z= 0.112 Angle : 0.563 12.832 12084 Z= 0.270 Chirality : 0.038 0.182 1438 Planarity : 0.005 0.061 1418 Dihedral : 8.293 76.267 1280 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.44 % Allowed : 10.33 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.27), residues: 1026 helix: 2.18 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.16 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 603 TYR 0.010 0.001 TYR A 824 PHE 0.011 0.001 PHE A 471 TRP 0.017 0.001 TRP A 492 HIS 0.002 0.000 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8856) covalent geometry : angle 0.56112 / 0.27 (12072) hydrogen bonds : bond 0.04229 / 2.74 ( 520) hydrogen bonds : angle 4.02236 / 2.93 ( 1506) Misc. bond : bond 0.00031 / 0.02 ( 2) link_BETA1-4 : bond 0.00408 / 0.20 ( 2) link_BETA1-4 : angle 0.99874 / 0.51 ( 6) link_NAG-ASN : bond 0.00040 / 0.02 ( 2) link_NAG-ASN : angle 1.77505 / 1.02 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1788.86 seconds wall clock time: 31 minutes 19.50 seconds (1879.50 seconds total)