Starting phenix.real_space_refine on Fri Oct 10 22:24:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6v_41082/10_2025/8t6v_41082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6v_41082/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8t6v_41082/10_2025/8t6v_41082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6v_41082/10_2025/8t6v_41082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t6v_41082/10_2025/8t6v_41082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6v_41082/10_2025/8t6v_41082.map" } 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-2.0-5842/lib/python3.9/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 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: 3.55, per 1000 atoms: 0.41 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: 0.83 Conformation dependent library (CDL) restraints added in 612.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.30 Time building geometry restraints manager: 1.07 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: 1.380 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.180 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:8.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 covalent geometry : bond 0.01171 ( 8856) covalent geometry : angle 1.86079 (12072) hydrogen bonds : bond 0.24835 ( 520) hydrogen bonds : angle 7.88430 ( 1506) Misc. bond : bond 0.01583 ( 2) link_BETA1-4 : bond 0.00468 ( 2) link_BETA1-4 : angle 0.77237 ( 6) link_NAG-ASN : bond 0.00880 ( 2) link_NAG-ASN : angle 4.65930 ( 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 : 0.334 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: 0.5692 time to fit residues: 58.9431 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 : 0.217 ------------------------------------------------------------------------------- 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... 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 = 0.2877 r_free = 0.2877 target = 0.053706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.043073 restraints weight = 68415.257| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 4.94 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 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 = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8862 Z= 0.157 Angle : 0.677 13.604 12084 Z= 0.330 Chirality : 0.041 0.137 1438 Planarity : 0.006 0.045 1418 Dihedral : 9.572 80.181 1834 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.00 % Allowed : 8.78 % 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 aren not related in a simple way. whole: 0.11 (0.25), residues: 1026 helix: 0.88 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.74 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 603 TYR 0.010 0.002 TYR B 519 PHE 0.012 0.002 PHE A 861 TRP 0.021 0.002 TRP A 492 HIS 0.001 0.000 HIS B 819 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8856) covalent geometry : angle 0.67615 (12072) hydrogen bonds : bond 0.06321 ( 520) hydrogen bonds : angle 4.75787 ( 1506) Misc. bond : bond 0.00096 ( 2) link_BETA1-4 : bond 0.00776 ( 2) link_BETA1-4 : angle 1.43125 ( 6) link_NAG-ASN : bond 0.00096 ( 2) link_NAG-ASN : angle 1.58618 ( 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 75 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 MET cc_start: 0.9822 (tpt) cc_final: 0.9560 (mmm) REVERT: A 664 MET cc_start: 0.9654 (OUTLIER) cc_final: 0.9444 (ttm) REVERT: A 741 MET cc_start: 0.9560 (mmt) cc_final: 0.9161 (mmm) REVERT: A 752 GLN cc_start: 0.9339 (mm110) cc_final: 0.8887 (pp30) REVERT: B 554 ASN cc_start: 0.8653 (m-40) cc_final: 0.8434 (t0) REVERT: B 559 MET cc_start: 0.8910 (mmm) cc_final: 0.8444 (mmm) REVERT: B 663 MET cc_start: 0.9813 (tpt) cc_final: 0.9544 (mmm) REVERT: B 664 MET cc_start: 0.9646 (OUTLIER) cc_final: 0.9431 (ttm) REVERT: B 741 MET cc_start: 0.9564 (mmt) cc_final: 0.9157 (mmm) REVERT: B 752 GLN cc_start: 0.9357 (mm110) cc_final: 0.8886 (pp30) outliers start: 18 outliers final: 3 residues processed: 71 average time/residue: 0.5697 time to fit residues: 43.4248 Evaluate side-chains 56 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 664 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.2877 r_free = 0.2877 target = 0.053725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.043143 restraints weight = 90898.706| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 5.50 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 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 = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8862 Z= 0.136 Angle : 0.601 8.869 12084 Z= 0.293 Chirality : 0.039 0.129 1438 Planarity : 0.006 0.065 1418 Dihedral : 9.083 86.966 1834 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.78 % Allowed : 8.00 % Favored : 90.22 % 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 aren not related in a simple way. whole: 1.17 (0.26), residues: 1026 helix: 1.78 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.54 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 603 TYR 0.012 0.001 TYR A 824 PHE 0.010 0.001 PHE A 836 TRP 0.016 0.001 TRP A 492 HIS 0.001 0.001 HIS A 547 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8856) covalent geometry : angle 0.59935 (12072) hydrogen bonds : bond 0.05009 ( 520) hydrogen bonds : angle 4.35748 ( 1506) Misc. bond : bond 0.00005 ( 2) link_BETA1-4 : bond 0.00695 ( 2) link_BETA1-4 : angle 0.98608 ( 6) link_NAG-ASN : bond 0.00033 ( 2) link_NAG-ASN : angle 2.05539 ( 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 73 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.208 Fit side-chains REVERT: A 429 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8747 (mt-10) REVERT: A 663 MET cc_start: 0.9840 (tpt) cc_final: 0.9573 (mmm) REVERT: A 705 ASP cc_start: 0.9288 (m-30) cc_final: 0.9009 (m-30) REVERT: A 741 MET cc_start: 0.9558 (mmt) cc_final: 0.9075 (mmm) REVERT: A 752 GLN cc_start: 0.9385 (mm110) cc_final: 0.8884 (pp30) REVERT: B 429 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8765 (mt-10) REVERT: B 559 MET cc_start: 0.8949 (mmm) cc_final: 0.8474 (mmm) REVERT: B 663 MET cc_start: 0.9839 (tpt) cc_final: 0.9568 (mmm) REVERT: B 705 ASP cc_start: 0.9293 (m-30) cc_final: 0.9007 (m-30) REVERT: B 741 MET cc_start: 0.9550 (mmt) cc_final: 0.9069 (mmm) REVERT: B 752 GLN cc_start: 0.9408 (mm110) cc_final: 0.8883 (pp30) outliers start: 16 outliers final: 6 residues processed: 69 average time/residue: 0.5544 time to fit residues: 41.0161 Evaluate side-chains 57 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 863 LEU 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 80 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.0060 chunk 4 optimal weight: 0.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- 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 = 0.2867 r_free = 0.2867 target = 0.053183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.042620 restraints weight = 90964.710| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 5.52 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 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 = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8862 Z= 0.147 Angle : 0.593 7.382 12084 Z= 0.287 Chirality : 0.039 0.126 1438 Planarity : 0.005 0.047 1418 Dihedral : 8.784 85.333 1834 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.67 % Allowed : 8.33 % Favored : 90.00 % 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 aren not related in a simple way. whole: 1.62 (0.27), residues: 1026 helix: 2.10 (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 0.010 0.001 ARG B 603 TYR 0.011 0.001 TYR B 519 PHE 0.012 0.001 PHE B 582 TRP 0.016 0.001 TRP A 492 HIS 0.002 0.000 HIS B 547 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8856) covalent geometry : angle 0.59081 (12072) hydrogen bonds : bond 0.04793 ( 520) hydrogen bonds : angle 4.26103 ( 1506) Misc. bond : bond 0.00035 ( 2) link_BETA1-4 : bond 0.00387 ( 2) link_BETA1-4 : angle 1.02511 ( 6) link_NAG-ASN : bond 0.00045 ( 2) link_NAG-ASN : angle 2.05766 ( 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 61 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.414 Fit side-chains REVERT: A 429 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8754 (mt-10) REVERT: A 586 MET cc_start: 0.9424 (mmp) cc_final: 0.9053 (mmm) REVERT: A 663 MET cc_start: 0.9850 (tpt) cc_final: 0.9606 (tpp) REVERT: A 705 ASP cc_start: 0.9286 (m-30) cc_final: 0.9023 (m-30) REVERT: A 721 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8375 (mtm) REVERT: A 741 MET cc_start: 0.9544 (mmt) cc_final: 0.8966 (mmm) REVERT: B 429 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8766 (mt-10) REVERT: B 663 MET cc_start: 0.9855 (tpt) cc_final: 0.9607 (tpp) REVERT: B 705 ASP cc_start: 0.9297 (m-30) cc_final: 0.9033 (m-30) REVERT: B 721 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8380 (mtm) REVERT: B 741 MET cc_start: 0.9544 (mmt) cc_final: 0.8970 (mmm) outliers start: 15 outliers final: 6 residues processed: 59 average time/residue: 0.6280 time to fit residues: 39.6439 Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 721 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 721 MET Chi-restraints excluded: chain B residue 863 LEU 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: 0.9980 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.053267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.042993 restraints weight = 74382.210| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 5.23 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 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 = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2489 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= 0.131 Angle : 0.580 6.822 12084 Z= 0.278 Chirality : 0.039 0.145 1438 Planarity : 0.005 0.058 1418 Dihedral : 8.628 80.797 1834 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.44 % Allowed : 9.44 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.27), residues: 1026 helix: 2.22 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.21 (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 519 PHE 0.011 0.001 PHE A 471 TRP 0.015 0.001 TRP A 492 HIS 0.002 0.000 HIS B 547 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8856) covalent geometry : angle 0.57812 (12072) hydrogen bonds : bond 0.04646 ( 520) hydrogen bonds : angle 4.16818 ( 1506) Misc. bond : bond 0.00040 ( 2) link_BETA1-4 : bond 0.00537 ( 2) link_BETA1-4 : angle 1.08966 ( 6) link_NAG-ASN : bond 0.00036 ( 2) link_NAG-ASN : angle 2.05157 ( 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 60 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.336 Fit side-chains REVERT: A 429 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8771 (mt-10) REVERT: A 586 MET cc_start: 0.9438 (mmp) cc_final: 0.9067 (mmm) REVERT: A 663 MET cc_start: 0.9856 (tpt) cc_final: 0.9619 (tpp) REVERT: A 664 MET cc_start: 0.9603 (ttm) cc_final: 0.9149 (mmm) REVERT: A 705 ASP cc_start: 0.9273 (m-30) cc_final: 0.9013 (m-30) REVERT: A 741 MET cc_start: 0.9583 (mmt) cc_final: 0.9136 (mmm) REVERT: B 429 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8764 (mt-10) REVERT: B 663 MET cc_start: 0.9856 (tpt) cc_final: 0.9614 (tpp) REVERT: B 664 MET cc_start: 0.9605 (ttm) cc_final: 0.9157 (mmm) REVERT: B 705 ASP cc_start: 0.9286 (m-30) cc_final: 0.9022 (m-30) REVERT: B 741 MET cc_start: 0.9586 (mmt) cc_final: 0.9142 (mmm) outliers start: 13 outliers final: 6 residues processed: 58 average time/residue: 0.5985 time to fit residues: 37.2171 Evaluate side-chains 51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 863 LEU 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: 1.9990 chunk 35 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2875 r_free = 0.2875 target = 0.053709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.043519 restraints weight = 62694.062| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 4.86 r_work (final): 0.2573 ------------------------------------------------------------------------------- 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 = 0.44 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2602 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= 0.120 Angle : 0.586 8.601 12084 Z= 0.278 Chirality : 0.038 0.145 1438 Planarity : 0.005 0.062 1418 Dihedral : 8.530 77.855 1834 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.44 % Allowed : 8.89 % 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 aren not related in a simple way. whole: 1.83 (0.27), residues: 1026 helix: 2.25 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.19 (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 519 PHE 0.011 0.001 PHE A 471 TRP 0.014 0.001 TRP A 492 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8856) covalent geometry : angle 0.58372 (12072) hydrogen bonds : bond 0.04495 ( 520) hydrogen bonds : angle 4.11813 ( 1506) Misc. bond : bond 0.00015 ( 2) link_BETA1-4 : bond 0.00480 ( 2) link_BETA1-4 : angle 1.06056 ( 6) link_NAG-ASN : bond 0.00014 ( 2) link_NAG-ASN : angle 2.03701 ( 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 62 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.335 Fit side-chains REVERT: A 429 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8762 (mt-10) REVERT: A 586 MET cc_start: 0.9424 (mmp) cc_final: 0.9049 (mmm) REVERT: A 603 ARG cc_start: 0.8315 (mtm110) cc_final: 0.7770 (ptp-110) REVERT: A 663 MET cc_start: 0.9853 (tpt) cc_final: 0.9602 (tpp) REVERT: A 664 MET cc_start: 0.9586 (ttm) cc_final: 0.9099 (mmm) REVERT: A 705 ASP cc_start: 0.9239 (m-30) cc_final: 0.8966 (m-30) REVERT: A 741 MET cc_start: 0.9568 (mmt) cc_final: 0.9159 (mmm) REVERT: B 429 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8758 (mt-10) REVERT: B 663 MET cc_start: 0.9854 (tpt) cc_final: 0.9599 (tpp) REVERT: B 664 MET cc_start: 0.9588 (ttm) cc_final: 0.9104 (mmm) REVERT: B 705 ASP cc_start: 0.9253 (m-30) cc_final: 0.8969 (m-30) REVERT: B 741 MET cc_start: 0.9567 (mmt) cc_final: 0.9157 (mmm) outliers start: 13 outliers final: 5 residues processed: 60 average time/residue: 0.5655 time to fit residues: 36.5737 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 : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 863 LEU 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: 0.0970 chunk 31 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.053993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.043941 restraints weight = 55705.758| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 4.69 r_work (final): 0.2593 ------------------------------------------------------------------------------- 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 = 0.44 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 = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8862 Z= 0.116 Angle : 0.576 10.569 12084 Z= 0.276 Chirality : 0.038 0.145 1438 Planarity : 0.005 0.053 1418 Dihedral : 8.358 73.560 1834 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.56 % Allowed : 8.78 % 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 aren not related in a simple way. whole: 1.84 (0.27), residues: 1026 helix: 2.24 (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 0.012 0.001 ARG B 603 TYR 0.010 0.001 TYR A 519 PHE 0.011 0.001 PHE A 471 TRP 0.013 0.001 TRP A 492 HIS 0.002 0.000 HIS A 547 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8856) covalent geometry : angle 0.57386 (12072) hydrogen bonds : bond 0.04321 ( 520) hydrogen bonds : angle 4.06225 ( 1506) Misc. bond : bond 0.00053 ( 2) link_BETA1-4 : bond 0.00614 ( 2) link_BETA1-4 : angle 1.12789 ( 6) link_NAG-ASN : bond 0.00023 ( 2) link_NAG-ASN : angle 2.00139 ( 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 61 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.299 Fit side-chains REVERT: A 429 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8703 (mt-10) REVERT: A 586 MET cc_start: 0.9426 (mmp) cc_final: 0.9100 (mmm) REVERT: A 663 MET cc_start: 0.9852 (tpt) cc_final: 0.9595 (tpp) REVERT: A 705 ASP cc_start: 0.9224 (m-30) cc_final: 0.8965 (m-30) REVERT: A 741 MET cc_start: 0.9555 (mmt) cc_final: 0.9148 (mmm) REVERT: B 429 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8693 (mt-10) REVERT: B 663 MET cc_start: 0.9854 (tpt) cc_final: 0.9593 (tpp) REVERT: B 705 ASP cc_start: 0.9241 (m-30) cc_final: 0.8983 (m-30) REVERT: B 741 MET cc_start: 0.9553 (mmt) cc_final: 0.9148 (mmm) outliers start: 14 outliers final: 8 residues processed: 56 average time/residue: 0.5864 time to fit residues: 35.1454 Evaluate side-chains 55 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 435 MET Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 863 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: 6.9990 chunk 49 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 86 optimal weight: 0.0470 chunk 87 optimal weight: 1.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- 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 = 0.2888 r_free = 0.2888 target = 0.054375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.043950 restraints weight = 80391.396| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 5.38 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 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 = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2854 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= 0.115 Angle : 0.570 11.584 12084 Z= 0.272 Chirality : 0.038 0.197 1438 Planarity : 0.006 0.094 1418 Dihedral : 8.254 70.137 1834 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.00 % Allowed : 9.33 % 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 aren not related in a simple way. whole: 1.88 (0.27), residues: 1026 helix: 2.26 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.10 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 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 0.001 0.000 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8856) covalent geometry : angle 0.56839 (12072) hydrogen bonds : bond 0.04227 ( 520) hydrogen bonds : angle 4.00896 ( 1506) Misc. bond : bond 0.00059 ( 2) link_BETA1-4 : bond 0.00474 ( 2) link_BETA1-4 : angle 1.07099 ( 6) link_NAG-ASN : bond 0.00006 ( 2) link_NAG-ASN : angle 1.99324 ( 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 56 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.337 Fit side-chains REVERT: A 429 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8728 (mt-10) REVERT: A 586 MET cc_start: 0.9402 (mmp) cc_final: 0.9088 (mmm) REVERT: A 663 MET cc_start: 0.9848 (tpt) cc_final: 0.9604 (tpp) REVERT: A 664 MET cc_start: 0.9650 (ttp) cc_final: 0.9209 (mmm) REVERT: A 705 ASP cc_start: 0.9249 (m-30) cc_final: 0.9006 (m-30) REVERT: A 741 MET cc_start: 0.9595 (mmt) cc_final: 0.9207 (mmm) REVERT: B 429 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8734 (mt-10) REVERT: B 603 ARG cc_start: 0.8931 (mtp-110) cc_final: 0.8673 (mtm110) REVERT: B 663 MET cc_start: 0.9851 (tpt) cc_final: 0.9603 (tpp) REVERT: B 664 MET cc_start: 0.9643 (ttp) cc_final: 0.9195 (mmm) REVERT: B 705 ASP cc_start: 0.9267 (m-30) cc_final: 0.9024 (m-30) REVERT: B 741 MET cc_start: 0.9594 (mmt) cc_final: 0.9211 (mmm) outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.6635 time to fit residues: 37.5970 Evaluate side-chains 54 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 435 MET Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 863 LEU 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: 0.8980 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 88 optimal weight: 0.0570 overall best weight: 1.0902 ------------------------------------------------------------------------------- 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 = 0.054096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.043501 restraints weight = 101611.355| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 5.86 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 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 = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8862 Z= 0.131 Angle : 0.582 11.893 12084 Z= 0.276 Chirality : 0.038 0.203 1438 Planarity : 0.005 0.051 1418 Dihedral : 8.147 68.177 1834 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.11 % Allowed : 9.22 % 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 aren not related in a simple way. whole: 1.92 (0.27), residues: 1026 helix: 2.28 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.07 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 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 0.001 0.000 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8856) covalent geometry : angle 0.58004 (12072) hydrogen bonds : bond 0.04233 ( 520) hydrogen bonds : angle 4.02747 ( 1506) Misc. bond : bond 0.00008 ( 2) link_BETA1-4 : bond 0.00448 ( 2) link_BETA1-4 : angle 1.03234 ( 6) link_NAG-ASN : bond 0.00032 ( 2) link_NAG-ASN : angle 1.99845 ( 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 57 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.352 Fit side-chains REVERT: A 429 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8758 (mt-10) REVERT: A 586 MET cc_start: 0.9392 (mmp) cc_final: 0.9087 (mmm) REVERT: A 603 ARG cc_start: 0.8367 (mtm110) cc_final: 0.7965 (ptp-110) REVERT: A 663 MET cc_start: 0.9831 (tpt) cc_final: 0.9564 (tpp) REVERT: A 705 ASP cc_start: 0.9275 (m-30) cc_final: 0.9042 (m-30) REVERT: A 741 MET cc_start: 0.9598 (mmt) cc_final: 0.9199 (mmm) REVERT: B 429 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8746 (mt-10) REVERT: B 603 ARG cc_start: 0.8920 (mtp-110) cc_final: 0.8548 (mtm-85) REVERT: B 663 MET cc_start: 0.9843 (tpt) cc_final: 0.9574 (tpp) REVERT: B 664 MET cc_start: 0.9634 (ttp) cc_final: 0.9310 (tpp) REVERT: B 705 ASP cc_start: 0.9295 (m-30) cc_final: 0.9065 (m-30) REVERT: B 741 MET cc_start: 0.9596 (mmt) cc_final: 0.9199 (mmm) outliers start: 10 outliers final: 7 residues processed: 54 average time/residue: 0.6099 time to fit residues: 35.4457 Evaluate side-chains 54 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 863 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 78 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 0.0020 chunk 33 optimal weight: 10.0000 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.2902 r_free = 0.2902 target = 0.054599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.044422 restraints weight = 72392.039| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 5.14 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8862 Z= 0.112 Angle : 0.568 12.609 12084 Z= 0.271 Chirality : 0.038 0.202 1438 Planarity : 0.005 0.055 1418 Dihedral : 7.891 62.229 1834 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.89 % Allowed : 9.44 % 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 aren not related in a simple way. whole: 1.87 (0.27), residues: 1026 helix: 2.24 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.17 (0.32), residues: 316 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 0.017 0.001 TRP B 492 HIS 0.002 0.000 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8856) covalent geometry : angle 0.56635 (12072) hydrogen bonds : bond 0.04065 ( 520) hydrogen bonds : angle 3.97824 ( 1506) Misc. bond : bond 0.00033 ( 2) link_BETA1-4 : bond 0.00445 ( 2) link_BETA1-4 : angle 1.05852 ( 6) link_NAG-ASN : bond 0.00015 ( 2) link_NAG-ASN : angle 1.95595 ( 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 62 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.347 Fit side-chains REVERT: A 429 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8689 (mt-10) REVERT: A 586 MET cc_start: 0.9408 (mmp) cc_final: 0.9113 (mmm) REVERT: A 603 ARG cc_start: 0.8398 (mtm110) cc_final: 0.7801 (ptt-90) REVERT: A 663 MET cc_start: 0.9814 (tpt) cc_final: 0.9541 (tpp) REVERT: A 664 MET cc_start: 0.9627 (ttp) cc_final: 0.9323 (tpp) REVERT: A 705 ASP cc_start: 0.9263 (m-30) cc_final: 0.9004 (m-30) REVERT: A 741 MET cc_start: 0.9586 (mmt) cc_final: 0.9201 (mmm) REVERT: B 429 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8702 (mt-10) REVERT: B 586 MET cc_start: 0.9128 (mmm) cc_final: 0.8888 (mmm) REVERT: B 603 ARG cc_start: 0.8890 (mtp-110) cc_final: 0.8660 (mtm110) REVERT: B 663 MET cc_start: 0.9817 (tpt) cc_final: 0.9539 (tpp) REVERT: B 664 MET cc_start: 0.9628 (ttp) cc_final: 0.9333 (tpp) REVERT: B 705 ASP cc_start: 0.9279 (m-30) cc_final: 0.9022 (m-30) REVERT: B 741 MET cc_start: 0.9578 (mmt) cc_final: 0.9194 (mmm) outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 0.5716 time to fit residues: 36.1740 Evaluate side-chains 51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 435 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 0.0060 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.2909 r_free = 0.2909 target = 0.054944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.044638 restraints weight = 82650.897| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 5.43 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8862 Z= 0.114 Angle : 0.571 12.299 12084 Z= 0.275 Chirality : 0.038 0.194 1438 Planarity : 0.005 0.052 1418 Dihedral : 7.754 59.837 1834 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.44 % Allowed : 10.11 % 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 aren not related in a simple way. whole: 1.89 (0.27), residues: 1026 helix: 2.24 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.11 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 603 TYR 0.009 0.001 TYR B 519 PHE 0.011 0.001 PHE B 526 TRP 0.016 0.001 TRP B 492 HIS 0.001 0.000 HIS B 819 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8856) covalent geometry : angle 0.56899 (12072) hydrogen bonds : bond 0.03998 ( 520) hydrogen bonds : angle 3.96690 ( 1506) Misc. bond : bond 0.00031 ( 2) link_BETA1-4 : bond 0.00491 ( 2) link_BETA1-4 : angle 1.04804 ( 6) link_NAG-ASN : bond 0.00011 ( 2) link_NAG-ASN : angle 1.94551 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.08 seconds wall clock time: 37 minutes 26.71 seconds (2246.71 seconds total)