Starting phenix.real_space_refine on Fri Feb 6 09:51:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gw2_51643/02_2026/9gw2_51643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gw2_51643/02_2026/9gw2_51643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gw2_51643/02_2026/9gw2_51643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gw2_51643/02_2026/9gw2_51643.map" model { file = "/net/cci-nas-00/data/ceres_data/9gw2_51643/02_2026/9gw2_51643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gw2_51643/02_2026/9gw2_51643.cif" } resolution = 4.84 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= 0.002 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: 6 Type Number sf(0) Gaussians P 250 5.49 5 S 32 5.16 5 C 7442 2.51 5 N 2440 2.21 5 O 2950 1.98 5 H 11011 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24125 Number of models: 1 Model: "" Number of chains: 12 Chain: "N" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 3982 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "O" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3923 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain: "T" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 3949 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "a" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1684 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "b" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "c" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1711 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "d" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1458 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "e" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1601 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "f" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1645 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "h" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1401 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "j" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 205 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Time building chain proxies: 4.56, per 1000 atoms: 0.19 Number of scatterers: 24125 At special positions: 0 Unit cell: (84, 119.7, 139.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 250 15.00 O 2950 8.00 N 2440 7.00 C 7442 6.00 H 11011 1.00 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=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 723.7 milliseconds 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 16 sheets defined 61.1% alpha, 6.3% beta 125 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'O' and resid 1452 through 1455 Processing helix chain 'O' and resid 1456 through 1466 Processing helix chain 'O' and resid 1488 through 1491 Processing helix chain 'O' and resid 1492 through 1497 Processing helix chain 'O' and resid 1505 through 1512 Processing helix chain 'O' and resid 1522 through 1526 Processing helix chain 'O' and resid 1535 through 1539 removed outlier: 3.557A pdb=" N CYS O1539 " --> pdb=" O GLY O1536 " (cutoff:3.500A) Processing helix chain 'O' and resid 1585 through 1599 Processing helix chain 'O' and resid 1622 through 1627 Processing helix chain 'a' and resid 45 through 58 Processing helix chain 'a' and resid 64 through 77 Processing helix chain 'a' and resid 86 through 115 removed outlier: 3.548A pdb=" N LEU a 110 " --> pdb=" O GLU a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 133 Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.517A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 17 through 23 Processing helix chain 'c' and resid 28 through 37 Processing helix chain 'c' and resid 47 through 74 removed outlier: 3.639A pdb=" N LEU c 66 " --> pdb=" O GLU c 62 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 91 Processing helix chain 'c' and resid 91 through 98 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 104 through 123 removed outlier: 4.092A pdb=" N LYS d 108 " --> pdb=" O GLY d 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 58 Processing helix chain 'e' and resid 64 through 78 removed outlier: 3.530A pdb=" N PHE e 68 " --> pdb=" O ARG e 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP e 78 " --> pdb=" O GLU e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 115 Processing helix chain 'e' and resid 121 through 133 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.761A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.520A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 17 through 23 Processing helix chain 'g' and resid 28 through 38 Processing helix chain 'g' and resid 46 through 74 removed outlier: 4.439A pdb=" N VAL g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 90 Processing helix chain 'g' and resid 91 through 98 removed outlier: 3.640A pdb=" N LYS g 96 " --> pdb=" O GLU g 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 37 through 49 removed outlier: 3.630A pdb=" N LYS h 43 " --> pdb=" O VAL h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 123 Processing helix chain 'j' and resid 940 through 945 removed outlier: 3.737A pdb=" N GLU j 944 " --> pdb=" O GLU j 940 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 1474 through 1475 removed outlier: 5.751A pdb=" N ASP O1474 " --> pdb=" O GLY O1621 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'O' and resid 1480 through 1481 removed outlier: 7.323A pdb=" N VAL O1480 " --> pdb=" O VAL O1583 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU O1613 " --> pdb=" O LEU O1609 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 1552 through 1556 Processing sheet with id=AA4, first strand: chain 'O' and resid 1575 through 1578 removed outlier: 6.651A pdb=" N PHE O1650 " --> pdb=" O VAL O1576 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU O1578 " --> pdb=" O VAL O1648 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL O1648 " --> pdb=" O GLU O1578 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 1628 through 1629 removed outlier: 6.462A pdb=" N ASN O1628 " --> pdb=" O PHE O1664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 1669 through 1670 Processing sheet with id=AA7, first strand: chain 'a' and resid 84 through 85 removed outlier: 7.151A pdb=" N ARG a 84 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'a' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.297A pdb=" N THR b 96 " --> pdb=" O THR g 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'c' and resid 43 through 44 removed outlier: 7.079A pdb=" N ARG c 43 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'c' and resid 78 through 79 Processing sheet with id=AB3, first strand: chain 'c' and resid 102 through 103 removed outlier: 6.726A pdb=" N THR c 102 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'e' and resid 84 through 85 removed outlier: 6.984A pdb=" N ARG e 84 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'e' and resid 119 through 120 Processing sheet with id=AB6, first strand: chain 'g' and resid 43 through 44 removed outlier: 7.250A pdb=" N ARG g 43 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'g' and resid 78 through 79 457 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 319 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 5.90 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 10995 1.02 - 1.22: 73 1.22 - 1.42: 6039 1.42 - 1.62: 7711 1.62 - 1.82: 49 Bond restraints: 24867 Sorted by residual: bond pdb=" C3' DC N 48 " pdb=" O3' DC N 48 " ideal model delta sigma weight residual 1.422 1.543 -0.121 3.00e-02 1.11e+03 1.62e+01 bond pdb=" O3' DC N 48 " pdb=" P DT N 49 " ideal model delta sigma weight residual 1.607 1.638 -0.031 1.50e-02 4.44e+03 4.28e+00 bond pdb=" C4' DC T 116 " pdb=" O4' DC T 116 " ideal model delta sigma weight residual 1.450 1.411 0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C4' DA N 109 " pdb=" O4' DA N 109 " ideal model delta sigma weight residual 1.450 1.417 0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" O5' DG N 4 " pdb=" C5' DG N 4 " ideal model delta sigma weight residual 1.423 1.471 -0.048 3.00e-02 1.11e+03 2.53e+00 ... (remaining 24862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.92: 44988 15.92 - 31.83: 0 31.83 - 47.75: 0 47.75 - 63.66: 0 63.66 - 79.58: 1 Bond angle restraints: 44989 Sorted by residual: angle pdb=" O3' DC N 48 " pdb=" P DT N 49 " pdb=" OP1 DT N 49 " ideal model delta sigma weight residual 108.00 28.42 79.58 3.00e+00 1.11e-01 7.04e+02 angle pdb=" C3' DC N 48 " pdb=" O3' DC N 48 " pdb=" P DT N 49 " ideal model delta sigma weight residual 120.20 132.89 -12.69 1.50e+00 4.44e-01 7.16e+01 angle pdb=" O3' DC N 48 " pdb=" C3' DC N 48 " pdb=" C2' DC N 48 " ideal model delta sigma weight residual 111.50 120.01 -8.51 1.50e+00 4.44e-01 3.22e+01 angle pdb=" O4' DC N 3 " pdb=" C1' DC N 3 " pdb=" N1 DC N 3 " ideal model delta sigma weight residual 108.40 116.07 -7.67 1.50e+00 4.44e-01 2.62e+01 angle pdb=" O3' DC N 48 " pdb=" P DT N 49 " pdb=" O5' DT N 49 " ideal model delta sigma weight residual 104.00 111.37 -7.37 1.50e+00 4.44e-01 2.41e+01 ... (remaining 44984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 9236 35.14 - 70.27: 1372 70.27 - 105.41: 17 105.41 - 140.54: 2 140.54 - 175.68: 1 Dihedral angle restraints: 10628 sinusoidal: 7331 harmonic: 3297 Sorted by residual: dihedral pdb=" C4' DG T 130 " pdb=" C3' DG T 130 " pdb=" O3' DG T 130 " pdb=" P DC T 131 " ideal model delta sinusoidal sigma weight residual 220.00 44.32 175.68 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CD ARG c 82 " pdb=" NE ARG c 82 " pdb=" CZ ARG c 82 " pdb=" NH1 ARG c 82 " ideal model delta sinusoidal sigma weight residual 0.00 32.61 -32.61 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" C4' DC T 118 " pdb=" C3' DC T 118 " pdb=" O3' DC T 118 " pdb=" P DG T 119 " ideal model delta sinusoidal sigma weight residual 220.00 81.57 138.43 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 10625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1774 0.105 - 0.210: 205 0.210 - 0.315: 170 0.315 - 0.420: 48 0.420 - 0.525: 16 Chirality restraints: 2213 Sorted by residual: chirality pdb=" P DT N 49 " pdb=" OP1 DT N 49 " pdb=" OP2 DT N 49 " pdb=" O5' DT N 49 " both_signs ideal model delta sigma weight residual True 2.35 1.82 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" P DT T 165 " pdb=" OP1 DT T 165 " pdb=" OP2 DT T 165 " pdb=" O5' DT T 165 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" P DT N 6 " pdb=" OP1 DT N 6 " pdb=" OP2 DT N 6 " pdb=" O5' DT N 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.46e+00 ... (remaining 2210 not shown) Planarity restraints: 2813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG c 82 " 0.492 9.50e-02 1.11e+02 1.65e-01 3.42e+01 pdb=" NE ARG c 82 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG c 82 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG c 82 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG c 82 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG c 82 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG c 82 " 0.014 2.00e-02 2.50e+03 pdb="HH21 ARG c 82 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG c 82 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG c 33 " 0.375 9.50e-02 1.11e+02 1.28e-01 3.02e+01 pdb=" NE ARG c 33 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG c 33 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG c 33 " -0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG c 33 " 0.027 2.00e-02 2.50e+03 pdb="HH11 ARG c 33 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG c 33 " 0.030 2.00e-02 2.50e+03 pdb="HH21 ARG c 33 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG c 33 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG g 18 " 0.134 9.50e-02 1.11e+02 5.63e-02 2.85e+01 pdb=" NE ARG g 18 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG g 18 " -0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG g 18 " -0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG g 18 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG g 18 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG g 18 " 0.045 2.00e-02 2.50e+03 pdb="HH21 ARG g 18 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG g 18 " 0.036 2.00e-02 2.50e+03 ... (remaining 2810 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.42: 10006 2.42 - 2.97: 49680 2.97 - 3.51: 59693 3.51 - 4.06: 84909 4.06 - 4.60: 121696 Nonbonded interactions: 325984 Sorted by model distance: nonbonded pdb=" O TYR c 40 " pdb=" HG SER d 78 " model vdw 1.877 2.450 nonbonded pdb=" HG1 THR d 90 " pdb=" OE1 GLU d 93 " model vdw 1.878 2.450 nonbonded pdb=" H2' DC N 46 " pdb=" H6 DC N 46 " model vdw 1.887 2.270 nonbonded pdb="HD12 LEU a 62 " pdb="HH21 ARG b 40 " model vdw 1.891 2.270 nonbonded pdb=" O LEU e 104 " pdb=" HG1 THR e 108 " model vdw 1.897 2.450 ... (remaining 325979 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 40 through 134) selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 16 through 118) selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 35 through 123) selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.470 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 28.240 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 : 0.006 0.121 13856 Z= 0.288 Angle : 1.827 79.578 19760 Z= 0.872 Chirality : 0.117 0.525 2213 Planarity : 0.017 0.217 1657 Dihedral : 23.821 175.677 5850 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.71 % Allowed : 2.00 % Favored : 97.29 % 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: -0.05 (0.25), residues: 983 helix: 0.69 (0.20), residues: 592 sheet: -1.64 (0.89), residues: 28 loop : -1.00 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.005 ARG c 82 TYR 0.037 0.007 TYR O1604 PHE 0.041 0.005 PHE j 948 TRP 0.037 0.006 TRP O1562 HIS 0.021 0.004 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00603 (13856) covalent geometry : angle 1.82687 (19760) hydrogen bonds : bond 0.12309 ( 776) hydrogen bonds : angle 4.81830 ( 1961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 467 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1452 ASP cc_start: 0.5855 (m-30) cc_final: 0.5068 (m-30) REVERT: O 1478 GLU cc_start: 0.7814 (pt0) cc_final: 0.7540 (pt0) REVERT: O 1482 LEU cc_start: 0.8103 (mp) cc_final: 0.6728 (tt) REVERT: O 1498 GLN cc_start: 0.8642 (tp40) cc_final: 0.8308 (tp40) REVERT: O 1526 MET cc_start: 0.8541 (mtm) cc_final: 0.8000 (mtm) REVERT: O 1574 THR cc_start: 0.7955 (m) cc_final: 0.7450 (m) REVERT: O 1587 LYS cc_start: 0.7549 (tttt) cc_final: 0.7269 (mttt) REVERT: O 1589 PHE cc_start: 0.7321 (t80) cc_final: 0.6971 (t80) REVERT: O 1595 GLU cc_start: 0.8620 (tt0) cc_final: 0.8214 (tt0) REVERT: O 1596 TYR cc_start: 0.5565 (m-10) cc_final: 0.5121 (m-10) REVERT: O 1612 ASP cc_start: 0.7656 (t0) cc_final: 0.7143 (t0) REVERT: O 1616 ASP cc_start: 0.5625 (t0) cc_final: 0.4493 (t0) REVERT: a 38 LYS cc_start: 0.7218 (pttp) cc_final: 0.6957 (pttt) REVERT: a 60 GLU cc_start: 0.8121 (pt0) cc_final: 0.7839 (pt0) REVERT: a 63 ILE cc_start: 0.8521 (mt) cc_final: 0.8306 (mm) REVERT: a 100 TYR cc_start: 0.7888 (t80) cc_final: 0.7616 (t80) REVERT: a 104 LEU cc_start: 0.8074 (tp) cc_final: 0.7812 (tt) REVERT: a 108 THR cc_start: 0.8578 (m) cc_final: 0.8072 (m) REVERT: a 130 ARG cc_start: 0.8479 (tpt90) cc_final: 0.8144 (tpt90) REVERT: b 25 ASN cc_start: 0.8854 (m-40) cc_final: 0.8626 (m110) REVERT: b 26 ILE cc_start: 0.8678 (tp) cc_final: 0.8184 (mt) REVERT: b 43 VAL cc_start: 0.8488 (t) cc_final: 0.8060 (m) REVERT: b 68 ASP cc_start: 0.8293 (m-30) cc_final: 0.7830 (m-30) REVERT: b 84 MET cc_start: 0.7072 (mmm) cc_final: 0.6827 (mmt) REVERT: c 43 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7686 (mtp85) REVERT: c 44 VAL cc_start: 0.8882 (t) cc_final: 0.8450 (p) REVERT: c 57 GLU cc_start: 0.7773 (tt0) cc_final: 0.7360 (tm-30) REVERT: c 62 GLU cc_start: 0.8210 (tp30) cc_final: 0.7679 (tp30) REVERT: c 85 GLN cc_start: 0.7580 (tp40) cc_final: 0.7310 (tp40) REVERT: d 41 VAL cc_start: 0.8124 (t) cc_final: 0.7758 (t) REVERT: d 45 LEU cc_start: 0.8766 (tp) cc_final: 0.8528 (tp) REVERT: d 52 THR cc_start: 0.8072 (m) cc_final: 0.7860 (m) REVERT: d 71 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7395 (tm-30) REVERT: d 85 LYS cc_start: 0.8248 (mttp) cc_final: 0.7702 (mtpt) REVERT: d 87 SER cc_start: 0.8571 (m) cc_final: 0.8126 (p) REVERT: d 120 LYS cc_start: 0.8391 (mttt) cc_final: 0.7982 (tptp) REVERT: e 56 GLN cc_start: 0.8499 (mt0) cc_final: 0.8192 (mt0) REVERT: e 57 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8059 (tmtt) REVERT: e 63 ILE cc_start: 0.8614 (mt) cc_final: 0.8207 (mt) REVERT: e 74 GLU cc_start: 0.7622 (tt0) cc_final: 0.7309 (tt0) REVERT: e 94 GLN cc_start: 0.8312 (tt0) cc_final: 0.7819 (tt0) REVERT: e 126 GLN cc_start: 0.8457 (mt0) cc_final: 0.8256 (mm-40) REVERT: f 25 ASN cc_start: 0.8455 (m-40) cc_final: 0.8208 (m-40) REVERT: f 74 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8397 (mm-30) REVERT: g 25 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8952 (mm-40) REVERT: g 36 ARG cc_start: 0.8646 (mtm110) cc_final: 0.8209 (ttp-110) REVERT: g 43 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7461 (mtm-85) REVERT: g 56 LEU cc_start: 0.8325 (mt) cc_final: 0.8065 (mt) REVERT: g 60 THR cc_start: 0.8978 (m) cc_final: 0.8777 (p) REVERT: g 62 GLU cc_start: 0.8861 (tp30) cc_final: 0.8644 (tp30) REVERT: g 85 GLN cc_start: 0.7287 (tp40) cc_final: 0.6978 (tp40) REVERT: g 93 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7230 (mt-10) REVERT: g 96 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8192 (tptt) REVERT: g 97 LEU cc_start: 0.9099 (tp) cc_final: 0.8893 (tt) REVERT: g 105 GLN cc_start: 0.7144 (mm-40) cc_final: 0.5899 (tp-100) REVERT: h 62 MET cc_start: 0.6944 (mmm) cc_final: 0.6702 (mmm) REVERT: h 85 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8139 (mptt) REVERT: h 86 ARG cc_start: 0.7779 (mmt180) cc_final: 0.7470 (mmm-85) REVERT: h 105 GLU cc_start: 0.7405 (tp30) cc_final: 0.7116 (tp30) REVERT: h 121 TYR cc_start: 0.8763 (t80) cc_final: 0.8549 (t80) outliers start: 6 outliers final: 2 residues processed: 470 average time/residue: 0.3635 time to fit residues: 219.9641 Evaluate side-chains 297 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 295 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 86 GLN a 109 ASN f 93 GLN g 25 GLN j 949 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.087071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.059457 restraints weight = 81578.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.062219 restraints weight = 36683.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.064015 restraints weight = 23145.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.065092 restraints weight = 17834.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.065777 restraints weight = 15429.748| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 13856 Z= 0.267 Angle : 0.697 5.012 19760 Z= 0.422 Chirality : 0.044 0.334 2213 Planarity : 0.006 0.051 1657 Dihedral : 28.275 171.057 3850 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.12 % Allowed : 2.59 % Favored : 97.29 % 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: 0.75 (0.26), residues: 983 helix: 1.42 (0.21), residues: 589 sheet: -0.23 (0.95), residues: 28 loop : -0.95 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O1532 TYR 0.013 0.002 TYR h 40 PHE 0.023 0.001 PHE O1668 TRP 0.004 0.001 TRP O1562 HIS 0.005 0.001 HIS f 75 Details of bonding type rmsd covalent geometry : bond 0.00573 (13856) covalent geometry : angle 0.69660 (19760) hydrogen bonds : bond 0.05423 ( 776) hydrogen bonds : angle 3.98689 ( 1961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1482 LEU cc_start: 0.8397 (mp) cc_final: 0.7352 (tt) REVERT: O 1538 TYR cc_start: 0.7892 (m-80) cc_final: 0.7685 (m-80) REVERT: O 1587 LYS cc_start: 0.7616 (tttt) cc_final: 0.7237 (mttt) REVERT: O 1589 PHE cc_start: 0.7575 (t80) cc_final: 0.7350 (t80) REVERT: O 1595 GLU cc_start: 0.8452 (tt0) cc_final: 0.8132 (tm-30) REVERT: O 1614 ILE cc_start: 0.6746 (mp) cc_final: 0.5773 (mp) REVERT: a 59 THR cc_start: 0.8474 (p) cc_final: 0.6631 (t) REVERT: a 60 GLU cc_start: 0.8416 (pt0) cc_final: 0.8097 (pt0) REVERT: a 63 ILE cc_start: 0.8511 (mt) cc_final: 0.8293 (mm) REVERT: a 94 GLN cc_start: 0.8268 (tt0) cc_final: 0.7990 (tt0) REVERT: a 108 THR cc_start: 0.8791 (m) cc_final: 0.8435 (m) REVERT: a 130 ARG cc_start: 0.8821 (tpt90) cc_final: 0.8363 (tpt90) REVERT: c 39 ASN cc_start: 0.7421 (m110) cc_final: 0.7210 (m110) REVERT: c 44 VAL cc_start: 0.8738 (t) cc_final: 0.8372 (p) REVERT: c 57 GLU cc_start: 0.7493 (tt0) cc_final: 0.7250 (tm-30) REVERT: c 62 GLU cc_start: 0.8272 (tp30) cc_final: 0.7774 (tp30) REVERT: c 79 ILE cc_start: 0.8257 (mt) cc_final: 0.7604 (tp) REVERT: c 86 LEU cc_start: 0.8296 (mt) cc_final: 0.8072 (mt) REVERT: d 33 ARG cc_start: 0.7601 (mtp85) cc_final: 0.7372 (mtp85) REVERT: d 37 TYR cc_start: 0.9061 (m-80) cc_final: 0.8743 (m-10) REVERT: d 41 VAL cc_start: 0.7881 (t) cc_final: 0.7675 (t) REVERT: d 71 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7733 (tm-30) REVERT: d 85 LYS cc_start: 0.8270 (mttp) cc_final: 0.7884 (mtpt) REVERT: d 86 ARG cc_start: 0.8021 (mmt-90) cc_final: 0.7586 (mmm-85) REVERT: d 113 GLU cc_start: 0.8682 (tp30) cc_final: 0.8282 (tm-30) REVERT: d 120 LYS cc_start: 0.8528 (mttt) cc_final: 0.7896 (tptp) REVERT: f 25 ASN cc_start: 0.8343 (m-40) cc_final: 0.7919 (m110) REVERT: f 74 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8728 (tt0) REVERT: g 85 GLN cc_start: 0.7314 (tp40) cc_final: 0.7032 (tp40) REVERT: g 91 ASP cc_start: 0.7571 (t70) cc_final: 0.7343 (t0) REVERT: g 96 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8269 (tptt) REVERT: g 105 GLN cc_start: 0.7906 (mm-40) cc_final: 0.6257 (mm-40) outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.2612 time to fit residues: 112.8729 Evaluate side-chains 257 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1643 ASN e 94 GLN g 25 GLN j 949 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.087025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.059148 restraints weight = 81321.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.061804 restraints weight = 37667.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.063490 restraints weight = 24201.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.064544 restraints weight = 19061.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.064900 restraints weight = 16652.266| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13856 Z= 0.239 Angle : 0.653 5.058 19760 Z= 0.400 Chirality : 0.042 0.173 2213 Planarity : 0.006 0.131 1657 Dihedral : 28.094 170.600 3850 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.24 % Allowed : 2.48 % Favored : 97.29 % 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: 0.78 (0.26), residues: 983 helix: 1.38 (0.21), residues: 597 sheet: -0.65 (1.31), residues: 18 loop : -0.83 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 30 TYR 0.016 0.002 TYR a 55 PHE 0.018 0.001 PHE O1668 TRP 0.003 0.001 TRP O1640 HIS 0.007 0.001 HIS f 75 Details of bonding type rmsd covalent geometry : bond 0.00514 (13856) covalent geometry : angle 0.65274 (19760) hydrogen bonds : bond 0.04650 ( 776) hydrogen bonds : angle 3.84087 ( 1961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1482 LEU cc_start: 0.8331 (mp) cc_final: 0.7189 (tt) REVERT: O 1587 LYS cc_start: 0.7764 (tttt) cc_final: 0.7331 (mttt) REVERT: O 1595 GLU cc_start: 0.8479 (tt0) cc_final: 0.8191 (tt0) REVERT: O 1596 TYR cc_start: 0.6008 (m-10) cc_final: 0.5555 (m-10) REVERT: O 1612 ASP cc_start: 0.7846 (t0) cc_final: 0.7628 (t70) REVERT: O 1619 GLN cc_start: 0.7427 (mp10) cc_final: 0.7222 (mp10) REVERT: a 59 THR cc_start: 0.8787 (p) cc_final: 0.7121 (t) REVERT: a 90 VAL cc_start: 0.8644 (t) cc_final: 0.8411 (t) REVERT: a 94 GLN cc_start: 0.8384 (tt0) cc_final: 0.7845 (tt0) REVERT: a 100 TYR cc_start: 0.7996 (t80) cc_final: 0.7738 (t80) REVERT: a 108 THR cc_start: 0.8778 (m) cc_final: 0.8562 (m) REVERT: a 130 ARG cc_start: 0.8789 (tpt90) cc_final: 0.8460 (tpt90) REVERT: b 26 ILE cc_start: 0.8483 (tp) cc_final: 0.8175 (mp) REVERT: c 44 VAL cc_start: 0.8607 (t) cc_final: 0.8175 (p) REVERT: c 62 GLU cc_start: 0.8057 (tp30) cc_final: 0.7710 (tp30) REVERT: c 86 LEU cc_start: 0.8233 (mt) cc_final: 0.7981 (mt) REVERT: d 71 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7706 (tm-30) REVERT: d 82 HIS cc_start: 0.7617 (t70) cc_final: 0.7216 (t70) REVERT: d 85 LYS cc_start: 0.8292 (mttp) cc_final: 0.7897 (mtpt) REVERT: d 86 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.7672 (mmm-85) REVERT: d 113 GLU cc_start: 0.8707 (tp30) cc_final: 0.8315 (tm-30) REVERT: d 120 LYS cc_start: 0.8496 (mttt) cc_final: 0.7873 (tptp) REVERT: f 51 TYR cc_start: 0.8756 (m-80) cc_final: 0.8299 (m-80) REVERT: f 74 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8805 (tt0) REVERT: g 96 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8296 (tptt) REVERT: g 105 GLN cc_start: 0.8139 (mm-40) cc_final: 0.6587 (mm-40) REVERT: h 62 MET cc_start: 0.7231 (tpp) cc_final: 0.7020 (tpp) REVERT: h 93 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7747 (mm-30) REVERT: h 100 LEU cc_start: 0.7978 (tp) cc_final: 0.7547 (tp) REVERT: h 105 GLU cc_start: 0.7420 (tp30) cc_final: 0.7097 (tp30) outliers start: 2 outliers final: 0 residues processed: 292 average time/residue: 0.2752 time to fit residues: 109.9901 Evaluate side-chains 246 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 24 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1643 ASN a 109 ASN b 25 ASN d 109 HIS g 90 ASN h 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.087318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.059933 restraints weight = 80864.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.062512 restraints weight = 37865.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.064080 restraints weight = 24416.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.065209 restraints weight = 19359.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.065757 restraints weight = 16854.384| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13856 Z= 0.219 Angle : 0.624 4.911 19760 Z= 0.382 Chirality : 0.041 0.151 2213 Planarity : 0.005 0.055 1657 Dihedral : 27.937 169.598 3850 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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 are not related in a simple way. whole: 0.89 (0.26), residues: 983 helix: 1.44 (0.21), residues: 597 sheet: -0.73 (1.33), residues: 18 loop : -0.73 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 30 TYR 0.013 0.001 TYR a 42 PHE 0.015 0.002 PHE O1668 TRP 0.003 0.001 TRP O1640 HIS 0.006 0.001 HIS f 75 Details of bonding type rmsd covalent geometry : bond 0.00467 (13856) covalent geometry : angle 0.62425 (19760) hydrogen bonds : bond 0.04315 ( 776) hydrogen bonds : angle 3.73046 ( 1961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1482 LEU cc_start: 0.8284 (mp) cc_final: 0.7174 (tt) REVERT: O 1587 LYS cc_start: 0.7770 (tttt) cc_final: 0.7360 (mttt) REVERT: O 1595 GLU cc_start: 0.8438 (tt0) cc_final: 0.8049 (tm-30) REVERT: a 59 THR cc_start: 0.8758 (p) cc_final: 0.7028 (t) REVERT: a 91 MET cc_start: 0.8618 (mmp) cc_final: 0.8184 (mmm) REVERT: a 94 GLN cc_start: 0.8386 (tt0) cc_final: 0.7810 (tt0) REVERT: a 100 TYR cc_start: 0.7877 (t80) cc_final: 0.7666 (t80) REVERT: a 130 ARG cc_start: 0.8859 (tpt90) cc_final: 0.8448 (tpt90) REVERT: b 26 ILE cc_start: 0.8511 (tp) cc_final: 0.8190 (mp) REVERT: c 58 TYR cc_start: 0.8175 (t80) cc_final: 0.7703 (t80) REVERT: c 62 GLU cc_start: 0.7933 (tp30) cc_final: 0.7567 (tp30) REVERT: c 86 LEU cc_start: 0.8267 (mt) cc_final: 0.8049 (mt) REVERT: d 71 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7665 (tm-30) REVERT: d 82 HIS cc_start: 0.7604 (t70) cc_final: 0.7170 (t70) REVERT: d 85 LYS cc_start: 0.8261 (mttp) cc_final: 0.7817 (mtpt) REVERT: d 86 ARG cc_start: 0.7954 (mmt-90) cc_final: 0.7583 (mmt-90) REVERT: d 113 GLU cc_start: 0.8778 (tp30) cc_final: 0.8336 (tm-30) REVERT: d 120 LYS cc_start: 0.8489 (mttt) cc_final: 0.7924 (tptp) REVERT: f 74 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8824 (tt0) REVERT: f 92 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7548 (tmm-80) REVERT: g 91 ASP cc_start: 0.7748 (t70) cc_final: 0.7428 (t0) REVERT: g 96 LYS cc_start: 0.8877 (ttmt) cc_final: 0.8353 (tptt) REVERT: g 105 GLN cc_start: 0.8095 (mm-40) cc_final: 0.6456 (mm-40) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2710 time to fit residues: 104.6730 Evaluate side-chains 244 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 23 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 25 ASN e 94 GLN g 69 ASN h 63 ASN j 949 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.085905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.057954 restraints weight = 82666.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.060653 restraints weight = 36721.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.062366 restraints weight = 23084.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.063468 restraints weight = 17923.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.064115 restraints weight = 15545.144| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 13856 Z= 0.297 Angle : 0.663 4.942 19760 Z= 0.404 Chirality : 0.045 0.152 2213 Planarity : 0.005 0.045 1657 Dihedral : 27.969 169.466 3850 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.24 % Allowed : 2.36 % Favored : 97.41 % 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: 0.51 (0.26), residues: 983 helix: 1.14 (0.21), residues: 597 sheet: -1.30 (1.29), residues: 16 loop : -0.85 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 79 TYR 0.021 0.002 TYR f 88 PHE 0.015 0.001 PHE O1668 TRP 0.004 0.001 TRP O1640 HIS 0.013 0.002 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00634 (13856) covalent geometry : angle 0.66274 (19760) hydrogen bonds : bond 0.04940 ( 776) hydrogen bonds : angle 4.03463 ( 1961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 259 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1482 LEU cc_start: 0.8287 (mp) cc_final: 0.7231 (tt) REVERT: O 1579 TYR cc_start: 0.7117 (t80) cc_final: 0.6474 (t80) REVERT: O 1587 LYS cc_start: 0.7772 (tttt) cc_final: 0.7338 (mttt) REVERT: O 1595 GLU cc_start: 0.8372 (tt0) cc_final: 0.8047 (tt0) REVERT: O 1596 TYR cc_start: 0.5790 (m-10) cc_final: 0.5497 (m-10) REVERT: O 1612 ASP cc_start: 0.7321 (t0) cc_final: 0.6942 (t0) REVERT: O 1653 THR cc_start: 0.8519 (m) cc_final: 0.7647 (m) REVERT: a 59 THR cc_start: 0.8787 (p) cc_final: 0.7002 (t) REVERT: a 61 LEU cc_start: 0.8550 (mm) cc_final: 0.7866 (mm) REVERT: a 91 MET cc_start: 0.8588 (mmp) cc_final: 0.8260 (tpp) REVERT: a 94 GLN cc_start: 0.8352 (tt0) cc_final: 0.7805 (tt0) REVERT: a 104 LEU cc_start: 0.7272 (tt) cc_final: 0.7017 (tt) REVERT: a 108 THR cc_start: 0.8563 (m) cc_final: 0.7977 (m) REVERT: a 124 ASP cc_start: 0.7572 (m-30) cc_final: 0.7148 (t70) REVERT: a 130 ARG cc_start: 0.8964 (tpt90) cc_final: 0.8510 (tpt90) REVERT: b 26 ILE cc_start: 0.8498 (tp) cc_final: 0.8255 (mt) REVERT: c 62 GLU cc_start: 0.8118 (tp30) cc_final: 0.7679 (tp30) REVERT: c 79 ILE cc_start: 0.8017 (mt) cc_final: 0.7407 (tp) REVERT: c 86 LEU cc_start: 0.8404 (mt) cc_final: 0.8159 (mt) REVERT: d 71 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7641 (tm-30) REVERT: d 82 HIS cc_start: 0.7588 (t70) cc_final: 0.7088 (t70) REVERT: d 113 GLU cc_start: 0.8858 (tp30) cc_final: 0.8323 (tm-30) REVERT: d 120 LYS cc_start: 0.8537 (mttt) cc_final: 0.7949 (tptp) REVERT: e 57 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8661 (ttmm) REVERT: f 74 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8907 (tt0) REVERT: f 92 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7556 (tmm-80) REVERT: g 91 ASP cc_start: 0.7823 (t70) cc_final: 0.7427 (t0) REVERT: g 94 LEU cc_start: 0.8245 (mm) cc_final: 0.7957 (mm) REVERT: g 96 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8350 (tptt) REVERT: g 105 GLN cc_start: 0.8218 (mm-40) cc_final: 0.6534 (mm-40) REVERT: h 90 THR cc_start: 0.8497 (p) cc_final: 0.8210 (p) REVERT: h 92 ARG cc_start: 0.8038 (ttp-110) cc_final: 0.7784 (ttp-110) outliers start: 2 outliers final: 0 residues processed: 259 average time/residue: 0.2392 time to fit residues: 87.5242 Evaluate side-chains 233 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 81 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 109 ASN b 25 ASN f 25 ASN h 63 ASN h 67 ASN j 949 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.087323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.059612 restraints weight = 81251.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.062400 restraints weight = 35861.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.064189 restraints weight = 22299.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.065172 restraints weight = 17184.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.065899 restraints weight = 15015.901| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13856 Z= 0.199 Angle : 0.603 4.657 19760 Z= 0.371 Chirality : 0.040 0.150 2213 Planarity : 0.005 0.049 1657 Dihedral : 27.867 169.877 3850 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.12 % Allowed : 1.42 % Favored : 98.47 % 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: 0.89 (0.26), residues: 983 helix: 1.44 (0.21), residues: 596 sheet: -1.06 (1.27), residues: 18 loop : -0.68 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 99 TYR 0.017 0.002 TYR g 58 PHE 0.013 0.001 PHE O1668 TRP 0.002 0.001 TRP O1640 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00423 (13856) covalent geometry : angle 0.60290 (19760) hydrogen bonds : bond 0.04161 ( 776) hydrogen bonds : angle 3.64428 ( 1961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1482 LEU cc_start: 0.8245 (mp) cc_final: 0.7166 (tt) REVERT: O 1500 GLU cc_start: 0.8734 (mm-30) cc_final: 0.7583 (tm-30) REVERT: O 1549 HIS cc_start: 0.7901 (p-80) cc_final: 0.7427 (p-80) REVERT: O 1587 LYS cc_start: 0.7766 (tttt) cc_final: 0.7309 (mttt) REVERT: O 1595 GLU cc_start: 0.8401 (tt0) cc_final: 0.8018 (tm-30) REVERT: O 1596 TYR cc_start: 0.5785 (m-10) cc_final: 0.5280 (m-10) REVERT: O 1607 MET cc_start: 0.5645 (tpp) cc_final: 0.5156 (tpp) REVERT: a 59 THR cc_start: 0.8779 (p) cc_final: 0.8344 (t) REVERT: a 61 LEU cc_start: 0.8516 (mm) cc_final: 0.7783 (mm) REVERT: a 91 MET cc_start: 0.8539 (mmp) cc_final: 0.8126 (mmm) REVERT: a 94 GLN cc_start: 0.8337 (tt0) cc_final: 0.8071 (tt0) REVERT: a 108 THR cc_start: 0.8593 (m) cc_final: 0.8010 (m) REVERT: a 124 ASP cc_start: 0.7612 (m-30) cc_final: 0.7290 (t70) REVERT: a 130 ARG cc_start: 0.8921 (tpt90) cc_final: 0.8459 (tpt90) REVERT: b 26 ILE cc_start: 0.8476 (tp) cc_final: 0.8261 (mt) REVERT: c 39 ASN cc_start: 0.7511 (m110) cc_final: 0.7305 (m110) REVERT: c 62 GLU cc_start: 0.8096 (tp30) cc_final: 0.7731 (tp30) REVERT: c 69 ASN cc_start: 0.8134 (m-40) cc_final: 0.7838 (m-40) REVERT: c 79 ILE cc_start: 0.8003 (mt) cc_final: 0.7395 (tp) REVERT: c 86 LEU cc_start: 0.8305 (mt) cc_final: 0.8087 (mt) REVERT: d 71 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7606 (tm-30) REVERT: d 82 HIS cc_start: 0.7557 (t70) cc_final: 0.7082 (t70) REVERT: d 113 GLU cc_start: 0.8796 (tp30) cc_final: 0.8278 (tm-30) REVERT: d 120 LYS cc_start: 0.8482 (mttt) cc_final: 0.7918 (tptp) REVERT: e 94 GLN cc_start: 0.8327 (tt0) cc_final: 0.7716 (tt0) REVERT: f 74 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8841 (tt0) REVERT: f 92 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7541 (tmm-80) REVERT: g 85 GLN cc_start: 0.7240 (tp40) cc_final: 0.6981 (tp40) REVERT: g 96 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8292 (tptt) REVERT: h 90 THR cc_start: 0.8435 (p) cc_final: 0.8067 (p) REVERT: h 92 ARG cc_start: 0.7896 (ttp-110) cc_final: 0.7667 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 268 average time/residue: 0.2496 time to fit residues: 94.9375 Evaluate side-chains 241 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 66 optimal weight: 0.0000 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 25 ASN h 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.087318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.059710 restraints weight = 80664.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.062451 restraints weight = 35799.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.064241 restraints weight = 22344.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.065237 restraints weight = 17242.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.065935 restraints weight = 15057.755| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13856 Z= 0.207 Angle : 0.609 4.755 19760 Z= 0.374 Chirality : 0.041 0.142 2213 Planarity : 0.005 0.056 1657 Dihedral : 27.819 169.356 3850 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 0.98 (0.26), residues: 983 helix: 1.50 (0.21), residues: 596 sheet: -1.01 (1.21), residues: 18 loop : -0.63 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG d 72 TYR 0.014 0.001 TYR g 58 PHE 0.013 0.001 PHE O1668 TRP 0.002 0.000 TRP O1640 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00441 (13856) covalent geometry : angle 0.60938 (19760) hydrogen bonds : bond 0.04242 ( 776) hydrogen bonds : angle 3.65406 ( 1961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1500 GLU cc_start: 0.8702 (mm-30) cc_final: 0.7591 (tm-30) REVERT: O 1544 PHE cc_start: 0.8494 (m-10) cc_final: 0.8270 (m-10) REVERT: O 1549 HIS cc_start: 0.7938 (p-80) cc_final: 0.7461 (p-80) REVERT: O 1587 LYS cc_start: 0.7663 (tttt) cc_final: 0.7223 (mttt) REVERT: O 1595 GLU cc_start: 0.8394 (tt0) cc_final: 0.8025 (tm-30) REVERT: O 1596 TYR cc_start: 0.5728 (m-10) cc_final: 0.5243 (m-10) REVERT: a 59 THR cc_start: 0.8884 (p) cc_final: 0.8415 (t) REVERT: a 60 GLU cc_start: 0.8520 (pt0) cc_final: 0.8274 (pt0) REVERT: a 61 LEU cc_start: 0.8473 (mm) cc_final: 0.7732 (mm) REVERT: a 91 MET cc_start: 0.8523 (mmp) cc_final: 0.8107 (mmm) REVERT: a 94 GLN cc_start: 0.8319 (tt0) cc_final: 0.7958 (tt0) REVERT: a 108 THR cc_start: 0.8752 (m) cc_final: 0.8533 (m) REVERT: a 130 ARG cc_start: 0.8902 (tpt90) cc_final: 0.8430 (tpt90) REVERT: c 39 ASN cc_start: 0.7494 (m110) cc_final: 0.7286 (m110) REVERT: c 62 GLU cc_start: 0.8008 (tp30) cc_final: 0.7706 (tp30) REVERT: c 69 ASN cc_start: 0.8145 (m-40) cc_final: 0.7858 (m-40) REVERT: c 79 ILE cc_start: 0.7971 (mt) cc_final: 0.7351 (tp) REVERT: c 86 LEU cc_start: 0.8305 (mt) cc_final: 0.8099 (mt) REVERT: d 82 HIS cc_start: 0.7549 (t70) cc_final: 0.7090 (t70) REVERT: d 113 GLU cc_start: 0.8780 (tp30) cc_final: 0.8270 (tm-30) REVERT: d 120 LYS cc_start: 0.8481 (mttt) cc_final: 0.7927 (tptp) REVERT: e 94 GLN cc_start: 0.8351 (tt0) cc_final: 0.7867 (tt0) REVERT: f 74 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8855 (tt0) REVERT: f 92 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7536 (tmm-80) REVERT: g 79 ILE cc_start: 0.8785 (mt) cc_final: 0.8582 (mt) REVERT: g 85 GLN cc_start: 0.7229 (tp40) cc_final: 0.6954 (tp40) REVERT: g 91 ASP cc_start: 0.7724 (t70) cc_final: 0.7128 (t0) REVERT: g 96 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8281 (tptt) REVERT: h 90 THR cc_start: 0.8500 (p) cc_final: 0.8229 (p) REVERT: h 92 ARG cc_start: 0.7897 (ttp-110) cc_final: 0.7693 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2605 time to fit residues: 98.5332 Evaluate side-chains 244 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 101 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 109 ASN ** e 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.087556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.059697 restraints weight = 81090.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.062472 restraints weight = 35981.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.064272 restraints weight = 22492.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.065385 restraints weight = 17425.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.065944 restraints weight = 15087.201| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13856 Z= 0.194 Angle : 0.600 4.753 19760 Z= 0.369 Chirality : 0.040 0.144 2213 Planarity : 0.005 0.056 1657 Dihedral : 27.738 169.388 3850 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 1.12 (0.27), residues: 983 helix: 1.63 (0.21), residues: 591 sheet: -1.12 (1.19), residues: 18 loop : -0.58 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG g 72 TYR 0.013 0.001 TYR d 40 PHE 0.013 0.001 PHE O1668 TRP 0.002 0.000 TRP O1640 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00417 (13856) covalent geometry : angle 0.60045 (19760) hydrogen bonds : bond 0.04116 ( 776) hydrogen bonds : angle 3.60398 ( 1961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1500 GLU cc_start: 0.8691 (mm-30) cc_final: 0.7597 (tm-30) REVERT: O 1549 HIS cc_start: 0.8004 (p-80) cc_final: 0.7499 (p-80) REVERT: O 1587 LYS cc_start: 0.7676 (tttt) cc_final: 0.7198 (mttt) REVERT: O 1595 GLU cc_start: 0.8398 (tt0) cc_final: 0.8025 (tm-30) REVERT: O 1596 TYR cc_start: 0.5755 (m-10) cc_final: 0.5255 (m-10) REVERT: a 59 THR cc_start: 0.8903 (p) cc_final: 0.8337 (t) REVERT: a 60 GLU cc_start: 0.8451 (pt0) cc_final: 0.8218 (pt0) REVERT: a 61 LEU cc_start: 0.8485 (mm) cc_final: 0.7744 (mm) REVERT: a 91 MET cc_start: 0.8494 (mmp) cc_final: 0.8108 (mmm) REVERT: a 94 GLN cc_start: 0.8289 (tt0) cc_final: 0.7922 (tt0) REVERT: a 104 LEU cc_start: 0.7174 (tt) cc_final: 0.6911 (tt) REVERT: a 108 THR cc_start: 0.8632 (m) cc_final: 0.8093 (m) REVERT: a 124 ASP cc_start: 0.7562 (m-30) cc_final: 0.7286 (t70) REVERT: a 130 ARG cc_start: 0.8941 (tpt90) cc_final: 0.8456 (tpt90) REVERT: b 78 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.8092 (mtp180) REVERT: c 62 GLU cc_start: 0.8120 (tp30) cc_final: 0.7815 (tp30) REVERT: c 69 ASN cc_start: 0.8155 (m-40) cc_final: 0.7866 (m-40) REVERT: c 79 ILE cc_start: 0.7922 (mt) cc_final: 0.7380 (tp) REVERT: c 86 LEU cc_start: 0.8340 (mt) cc_final: 0.8078 (mt) REVERT: d 71 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7555 (tm-30) REVERT: d 82 HIS cc_start: 0.7648 (t70) cc_final: 0.7198 (t70) REVERT: d 86 ARG cc_start: 0.8243 (mmt-90) cc_final: 0.7747 (mmm-85) REVERT: d 113 GLU cc_start: 0.8761 (tp30) cc_final: 0.8285 (tm-30) REVERT: d 120 LYS cc_start: 0.8480 (mttt) cc_final: 0.7931 (tptp) REVERT: f 92 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7529 (tmm-80) REVERT: g 85 GLN cc_start: 0.7263 (tp40) cc_final: 0.6993 (tp40) REVERT: g 91 ASP cc_start: 0.7714 (t70) cc_final: 0.7345 (t0) REVERT: g 96 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8287 (tptt) REVERT: h 90 THR cc_start: 0.8490 (p) cc_final: 0.8213 (p) REVERT: h 93 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7959 (mm-30) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2615 time to fit residues: 97.8632 Evaluate side-chains 245 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 25 ASN ** e 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 94 GLN h 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.086165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.058437 restraints weight = 82163.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.061131 restraints weight = 36534.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.062904 restraints weight = 22919.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.063892 restraints weight = 17722.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.064563 restraints weight = 15501.478| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 13856 Z= 0.258 Angle : 0.636 4.938 19760 Z= 0.389 Chirality : 0.043 0.142 2213 Planarity : 0.005 0.059 1657 Dihedral : 27.792 169.292 3850 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: 0.73 (0.26), residues: 983 helix: 1.33 (0.21), residues: 595 sheet: -1.44 (1.15), residues: 18 loop : -0.77 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG d 99 TYR 0.012 0.002 TYR d 40 PHE 0.013 0.001 PHE O1668 TRP 0.003 0.001 TRP O1640 HIS 0.008 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00553 (13856) covalent geometry : angle 0.63573 (19760) hydrogen bonds : bond 0.04686 ( 776) hydrogen bonds : angle 3.89165 ( 1961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1513 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7123 (mp0) REVERT: O 1587 LYS cc_start: 0.7693 (tttt) cc_final: 0.7198 (mttt) REVERT: O 1595 GLU cc_start: 0.8367 (tt0) cc_final: 0.8031 (tt0) REVERT: O 1596 TYR cc_start: 0.5738 (m-10) cc_final: 0.5531 (m-10) REVERT: a 59 THR cc_start: 0.8807 (p) cc_final: 0.8313 (t) REVERT: a 61 LEU cc_start: 0.8435 (mm) cc_final: 0.7756 (mm) REVERT: a 74 GLU cc_start: 0.8067 (tt0) cc_final: 0.7472 (tt0) REVERT: a 91 MET cc_start: 0.8485 (mmp) cc_final: 0.8190 (mmm) REVERT: a 94 GLN cc_start: 0.8321 (tt0) cc_final: 0.7996 (tt0) REVERT: a 130 ARG cc_start: 0.8980 (tpt90) cc_final: 0.8501 (tpt90) REVERT: b 25 ASN cc_start: 0.8961 (m-40) cc_final: 0.8712 (m110) REVERT: c 62 GLU cc_start: 0.8120 (tp30) cc_final: 0.7762 (tp30) REVERT: c 69 ASN cc_start: 0.8160 (m-40) cc_final: 0.7895 (m-40) REVERT: c 79 ILE cc_start: 0.7808 (mt) cc_final: 0.7175 (tp) REVERT: c 86 LEU cc_start: 0.8323 (mt) cc_final: 0.8119 (mt) REVERT: d 71 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7607 (tm-30) REVERT: d 82 HIS cc_start: 0.7632 (t70) cc_final: 0.7203 (t70) REVERT: d 86 ARG cc_start: 0.8199 (mmt-90) cc_final: 0.7794 (mmm-85) REVERT: d 113 GLU cc_start: 0.8824 (tp30) cc_final: 0.8352 (tm-30) REVERT: d 120 LYS cc_start: 0.8490 (mttt) cc_final: 0.7986 (tptp) REVERT: e 94 GLN cc_start: 0.8073 (tt0) cc_final: 0.7655 (tt0) REVERT: g 85 GLN cc_start: 0.7330 (tp40) cc_final: 0.7080 (tp40) REVERT: g 96 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8339 (tptt) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2537 time to fit residues: 92.0123 Evaluate side-chains 229 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.0170 chunk 92 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 90 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 109 ASN h 63 ASN h 67 ASN j 949 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.089089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.061545 restraints weight = 79787.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.064347 restraints weight = 34745.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.066193 restraints weight = 21554.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.067327 restraints weight = 16580.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.067887 restraints weight = 14357.167| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13856 Z= 0.156 Angle : 0.588 5.107 19760 Z= 0.361 Chirality : 0.038 0.142 2213 Planarity : 0.005 0.059 1657 Dihedral : 27.667 169.411 3850 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.12 % Allowed : 0.47 % Favored : 99.41 % 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: 1.34 (0.27), residues: 983 helix: 1.91 (0.21), residues: 584 sheet: -1.03 (1.19), residues: 18 loop : -0.62 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG d 72 TYR 0.021 0.002 TYR f 88 PHE 0.012 0.001 PHE O1668 TRP 0.001 0.000 TRP O1460 HIS 0.005 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00341 (13856) covalent geometry : angle 0.58750 (19760) hydrogen bonds : bond 0.03881 ( 776) hydrogen bonds : angle 3.44525 ( 1961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1500 GLU cc_start: 0.8663 (mm-30) cc_final: 0.7572 (tm-30) REVERT: O 1587 LYS cc_start: 0.7679 (tttt) cc_final: 0.7222 (mttt) REVERT: O 1595 GLU cc_start: 0.8376 (tt0) cc_final: 0.8013 (tm-30) REVERT: a 59 THR cc_start: 0.8827 (p) cc_final: 0.8336 (t) REVERT: a 74 GLU cc_start: 0.8097 (tt0) cc_final: 0.7728 (tt0) REVERT: a 130 ARG cc_start: 0.8972 (tpt90) cc_final: 0.8501 (tpt90) REVERT: c 62 GLU cc_start: 0.8158 (tp30) cc_final: 0.7852 (tp30) REVERT: d 68 ASP cc_start: 0.8519 (t70) cc_final: 0.8102 (t0) REVERT: d 82 HIS cc_start: 0.7673 (t70) cc_final: 0.7251 (t70) REVERT: d 113 GLU cc_start: 0.8778 (tp30) cc_final: 0.8296 (tm-30) REVERT: d 120 LYS cc_start: 0.8455 (mttt) cc_final: 0.7906 (tptp) REVERT: e 94 GLN cc_start: 0.8051 (tt0) cc_final: 0.7823 (tt0) REVERT: f 92 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7580 (tmm-80) REVERT: g 85 GLN cc_start: 0.7253 (tp40) cc_final: 0.7008 (tp40) REVERT: g 96 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8231 (tptt) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.2404 time to fit residues: 93.8295 Evaluate side-chains 242 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 101 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 25 ASN h 63 ASN h 67 ASN j 949 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.087006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.059824 restraints weight = 81386.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.062449 restraints weight = 36767.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.064156 restraints weight = 23286.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.065123 restraints weight = 18174.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.065763 restraints weight = 15936.401| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13856 Z= 0.233 Angle : 0.620 4.790 19760 Z= 0.380 Chirality : 0.042 0.140 2213 Planarity : 0.005 0.089 1657 Dihedral : 27.714 168.988 3850 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.12 % Allowed : 0.59 % Favored : 99.29 % 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: 0.98 (0.26), residues: 983 helix: 1.57 (0.21), residues: 587 sheet: -1.39 (1.13), residues: 18 loop : -0.70 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 72 TYR 0.019 0.002 TYR f 88 PHE 0.013 0.001 PHE O1668 TRP 0.003 0.001 TRP O1640 HIS 0.011 0.001 HIS O1491 Details of bonding type rmsd covalent geometry : bond 0.00500 (13856) covalent geometry : angle 0.62027 (19760) hydrogen bonds : bond 0.04446 ( 776) hydrogen bonds : angle 3.78049 ( 1961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4091.03 seconds wall clock time: 70 minutes 32.34 seconds (4232.34 seconds total)