Starting phenix.real_space_refine on Sat Nov 16 20:38:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/11_2024/8ox0_17251.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/11_2024/8ox0_17251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/11_2024/8ox0_17251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/11_2024/8ox0_17251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/11_2024/8ox0_17251.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/11_2024/8ox0_17251.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 14 5.16 5 C 6773 2.51 5 N 2308 2.21 5 O 2886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12271 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "J" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 3064 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "I" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2881 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 7.43, per 1000 atoms: 0.61 Number of scatterers: 12271 At special positions: 0 Unit cell: (92.71, 118.99, 125.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 290 15.00 O 2886 8.00 N 2308 7.00 C 6773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.0 seconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1470 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 70.8% alpha, 3.0% beta 143 base pairs and 278 stacking pairs defined. Time for finding SS restraints: 5.96 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.712A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.519A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.490A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.530A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.524A pdb=" N SER D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.624A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.009A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.852A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.802A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.512A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.899A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.567A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.089A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.657A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.836A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 409 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 355 hydrogen bonds 706 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 278 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1694 1.33 - 1.45: 4763 1.45 - 1.57: 5960 1.57 - 1.69: 578 1.69 - 1.81: 24 Bond restraints: 13019 Sorted by residual: bond pdb=" C ARG F 95 " pdb=" O ARG F 95 " ideal model delta sigma weight residual 1.233 1.203 0.030 1.15e-02 7.56e+03 7.02e+00 bond pdb=" CA GLU E 105 " pdb=" C GLU E 105 " ideal model delta sigma weight residual 1.524 1.557 -0.033 1.27e-02 6.20e+03 6.83e+00 bond pdb=" CA LYS F 31 " pdb=" C LYS F 31 " ideal model delta sigma weight residual 1.520 1.550 -0.029 1.23e-02 6.61e+03 5.75e+00 bond pdb=" C PRO G 26 " pdb=" O PRO G 26 " ideal model delta sigma weight residual 1.235 1.217 0.018 7.90e-03 1.60e+04 4.96e+00 bond pdb=" CA GLU A 105 " pdb=" C GLU A 105 " ideal model delta sigma weight residual 1.524 1.551 -0.028 1.27e-02 6.20e+03 4.74e+00 ... (remaining 13014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 16684 1.30 - 2.60: 1752 2.60 - 3.89: 341 3.89 - 5.19: 20 5.19 - 6.49: 7 Bond angle restraints: 18804 Sorted by residual: angle pdb=" O3' DA I 14 " pdb=" C3' DA I 14 " pdb=" C2' DA I 14 " ideal model delta sigma weight residual 111.50 106.11 5.39 1.50e+00 4.44e-01 1.29e+01 angle pdb=" O3' DT J -26 " pdb=" C3' DT J -26 " pdb=" C2' DT J -26 " ideal model delta sigma weight residual 111.50 106.16 5.34 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C4' DT I -18 " pdb=" C3' DT I -18 " pdb=" O3' DT I -18 " ideal model delta sigma weight residual 110.00 114.63 -4.63 1.50e+00 4.44e-01 9.51e+00 angle pdb=" O3' DA I 44 " pdb=" C3' DA I 44 " pdb=" C2' DA I 44 " ideal model delta sigma weight residual 111.50 107.05 4.45 1.50e+00 4.44e-01 8.78e+00 angle pdb=" C2' DT J -26 " pdb=" C1' DT J -26 " pdb=" N1 DT J -26 " ideal model delta sigma weight residual 113.50 117.90 -4.40 1.50e+00 4.44e-01 8.61e+00 ... (remaining 18799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 5747 35.46 - 70.92: 1401 70.92 - 106.38: 4 106.38 - 141.83: 0 141.83 - 177.29: 3 Dihedral angle restraints: 7155 sinusoidal: 4876 harmonic: 2279 Sorted by residual: dihedral pdb=" C4' DT I -18 " pdb=" C3' DT I -18 " pdb=" O3' DT I -18 " pdb=" P DA I -17 " ideal model delta sinusoidal sigma weight residual 220.00 42.71 177.29 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J -71 " pdb=" C3' DA J -71 " pdb=" O3' DA J -71 " pdb=" P DT J -70 " ideal model delta sinusoidal sigma weight residual 220.00 43.55 176.45 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 22 " pdb=" C3' DC I 22 " pdb=" O3' DC I 22 " pdb=" P DC I 23 " ideal model delta sinusoidal sigma weight residual 220.00 64.11 155.89 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 7152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1307 0.048 - 0.096: 634 0.096 - 0.144: 144 0.144 - 0.193: 36 0.193 - 0.241: 8 Chirality restraints: 2129 Sorted by residual: chirality pdb=" C3' DC I 22 " pdb=" C4' DC I 22 " pdb=" O3' DC I 22 " pdb=" C2' DC I 22 " both_signs ideal model delta sigma weight residual False -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C3' DA J -71 " pdb=" C4' DA J -71 " pdb=" O3' DA J -71 " pdb=" C2' DA J -71 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ARG C 88 " pdb=" N ARG C 88 " pdb=" C ARG C 88 " pdb=" CB ARG C 88 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2126 not shown) Planarity restraints: 1375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -35 " -0.034 2.00e-02 2.50e+03 1.43e-02 6.12e+00 pdb=" N9 DG J -35 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG J -35 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG J -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG J -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG J -35 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG J -35 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG J -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG J -35 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG J -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG J -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG J -35 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 15 " -0.033 2.00e-02 2.50e+03 1.38e-02 5.74e+00 pdb=" N9 DG J 15 " 0.028 2.00e-02 2.50e+03 pdb=" C8 DG J 15 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG J 15 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG J 15 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 15 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG J 15 " -0.015 2.00e-02 2.50e+03 pdb=" N1 DG J 15 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG J 15 " 0.007 2.00e-02 2.50e+03 pdb=" N2 DG J 15 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG J 15 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG J 15 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 64 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ASN B 64 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN B 64 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 65 " -0.013 2.00e-02 2.50e+03 ... (remaining 1372 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 424 2.70 - 3.25: 10392 3.25 - 3.80: 22837 3.80 - 4.35: 29973 4.35 - 4.90: 41615 Nonbonded interactions: 105241 Sorted by model distance: nonbonded pdb=" O ARG F 23 " pdb=" OD1 ASP F 24 " model vdw 2.156 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.316 3.040 nonbonded pdb=" NH2 ARG B 35 " pdb=" OP2 DG J 8 " model vdw 2.336 3.120 nonbonded pdb=" N2 DG J 21 " pdb=" O2 DC I -21 " model vdw 2.340 2.496 ... (remaining 105236 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 37 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 17 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.450 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 0.007 0.035 13019 Z= 0.405 Angle : 0.876 6.490 18804 Z= 0.568 Chirality : 0.058 0.241 2129 Planarity : 0.005 0.042 1375 Dihedral : 27.178 177.293 5685 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.28), residues: 771 helix: 1.92 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.55 (0.32), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.019 0.004 PHE H 67 TYR 0.018 0.004 TYR B 51 ARG 0.011 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8164 (ttt180) cc_final: 0.7737 (ttp-110) REVERT: A 64 LYS cc_start: 0.7812 (mttt) cc_final: 0.7605 (mttp) REVERT: B 91 LYS cc_start: 0.7694 (tttp) cc_final: 0.7174 (ttpt) REVERT: C 90 ASP cc_start: 0.7168 (t0) cc_final: 0.6927 (t70) REVERT: C 91 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7506 (mp0) REVERT: D 48 ASP cc_start: 0.8654 (m-30) cc_final: 0.8277 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7629 (mtm180) cc_final: 0.7230 (mtt90) REVERT: E 68 GLN cc_start: 0.7502 (tt0) cc_final: 0.7122 (tt0) REVERT: F 93 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7141 (mp10) REVERT: G 15 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7282 (mtpt) REVERT: G 73 ASN cc_start: 0.7834 (m110) cc_final: 0.7588 (m110) REVERT: G 75 LYS cc_start: 0.8046 (mttt) cc_final: 0.7783 (mtpp) REVERT: G 90 ASP cc_start: 0.7528 (t0) cc_final: 0.7269 (t0) REVERT: G 95 LYS cc_start: 0.8030 (tttt) cc_final: 0.7660 (tppt) REVERT: G 99 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7242 (mpt180) REVERT: H 31 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7752 (mttp) REVERT: H 105 LYS cc_start: 0.7467 (ttpt) cc_final: 0.7063 (mmtm) outliers start: 0 outliers final: 1 residues processed: 148 average time/residue: 2.0743 time to fit residues: 323.0417 Evaluate side-chains 129 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13019 Z= 0.207 Angle : 0.596 6.802 18804 Z= 0.363 Chirality : 0.035 0.143 2129 Planarity : 0.004 0.039 1375 Dihedral : 30.900 179.789 4095 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.22 % Allowed : 9.31 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.29), residues: 771 helix: 2.38 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.47 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE F 61 TYR 0.010 0.001 TYR H 37 ARG 0.003 0.000 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7838 (ttt180) cc_final: 0.7491 (ttp-110) REVERT: A 64 LYS cc_start: 0.7807 (mttt) cc_final: 0.7604 (mttm) REVERT: B 91 LYS cc_start: 0.7661 (tttp) cc_final: 0.7128 (ttpt) REVERT: C 90 ASP cc_start: 0.7126 (t0) cc_final: 0.6920 (t70) REVERT: C 91 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7387 (mp0) REVERT: D 48 ASP cc_start: 0.8627 (m-30) cc_final: 0.8254 (p0) REVERT: D 96 ARG cc_start: 0.7562 (mtm180) cc_final: 0.7298 (mtm-85) REVERT: E 59 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: E 68 GLN cc_start: 0.7471 (tt0) cc_final: 0.7137 (tt0) REVERT: E 133 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7075 (mt-10) REVERT: F 93 GLN cc_start: 0.7444 (mm-40) cc_final: 0.7067 (mp10) REVERT: G 15 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7261 (mtpt) REVERT: G 73 ASN cc_start: 0.7382 (m110) cc_final: 0.7116 (m110) REVERT: G 90 ASP cc_start: 0.7251 (t0) cc_final: 0.6994 (t0) REVERT: G 95 LYS cc_start: 0.8049 (tttt) cc_final: 0.7688 (tppt) REVERT: G 99 ARG cc_start: 0.7671 (mmm160) cc_final: 0.7187 (mpt180) REVERT: H 31 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7689 (mttp) REVERT: H 105 LYS cc_start: 0.7394 (ttpt) cc_final: 0.6996 (mmtm) outliers start: 8 outliers final: 4 residues processed: 133 average time/residue: 2.0623 time to fit residues: 288.6002 Evaluate side-chains 132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 13019 Z= 0.483 Angle : 0.669 7.969 18804 Z= 0.399 Chirality : 0.043 0.162 2129 Planarity : 0.005 0.038 1375 Dihedral : 31.321 178.876 4095 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.98 % Allowed : 9.62 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.29), residues: 771 helix: 2.34 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.60 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.014 0.002 PHE A 104 TYR 0.014 0.002 TYR E 54 ARG 0.005 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7854 (ttt180) cc_final: 0.7502 (ttp-110) REVERT: A 59 GLU cc_start: 0.7789 (pm20) cc_final: 0.7560 (pm20) REVERT: B 91 LYS cc_start: 0.7673 (tttp) cc_final: 0.7458 (ttmm) REVERT: C 90 ASP cc_start: 0.7275 (t0) cc_final: 0.7035 (t70) REVERT: C 91 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7399 (mp0) REVERT: D 48 ASP cc_start: 0.8608 (m-30) cc_final: 0.8261 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7592 (mtm180) cc_final: 0.7294 (mtm-85) REVERT: E 133 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: F 93 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7076 (mp10) REVERT: G 15 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7338 (mtpt) REVERT: G 90 ASP cc_start: 0.7272 (t0) cc_final: 0.7025 (t0) REVERT: G 95 LYS cc_start: 0.8050 (tttt) cc_final: 0.7687 (tppt) REVERT: G 99 ARG cc_start: 0.7591 (mmm160) cc_final: 0.7179 (mpt180) REVERT: H 31 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7761 (mttp) REVERT: H 105 LYS cc_start: 0.7456 (ttpt) cc_final: 0.7000 (mmtm) outliers start: 13 outliers final: 8 residues processed: 133 average time/residue: 2.1128 time to fit residues: 295.7097 Evaluate side-chains 131 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13019 Z= 0.280 Angle : 0.627 7.490 18804 Z= 0.379 Chirality : 0.038 0.150 2129 Planarity : 0.004 0.039 1375 Dihedral : 31.321 179.414 4095 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.29 % Allowed : 10.38 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.29), residues: 771 helix: 2.43 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.60 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.002 PHE A 67 TYR 0.012 0.002 TYR H 37 ARG 0.004 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.984 Fit side-chains REVERT: A 53 ARG cc_start: 0.7843 (ttt180) cc_final: 0.7462 (ttp-110) REVERT: A 59 GLU cc_start: 0.7815 (pm20) cc_final: 0.7614 (pm20) REVERT: B 91 LYS cc_start: 0.7657 (tttp) cc_final: 0.7442 (ttmm) REVERT: C 90 ASP cc_start: 0.7287 (t0) cc_final: 0.7051 (t70) REVERT: C 91 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7402 (mp0) REVERT: D 48 ASP cc_start: 0.8617 (m-30) cc_final: 0.8271 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7567 (mtm180) cc_final: 0.7293 (mtm-85) REVERT: E 68 GLN cc_start: 0.7483 (tt0) cc_final: 0.7123 (tt0) REVERT: E 133 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6930 (mt-10) REVERT: F 93 GLN cc_start: 0.7400 (mm-40) cc_final: 0.7049 (mp10) REVERT: G 15 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7335 (mtpt) REVERT: G 90 ASP cc_start: 0.7271 (t0) cc_final: 0.7031 (t0) REVERT: G 95 LYS cc_start: 0.8039 (tttt) cc_final: 0.7675 (tppt) REVERT: G 99 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7173 (mpt180) REVERT: H 31 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7723 (mttp) REVERT: H 105 LYS cc_start: 0.7435 (ttpt) cc_final: 0.6993 (mmtm) outliers start: 15 outliers final: 8 residues processed: 131 average time/residue: 2.0246 time to fit residues: 279.5750 Evaluate side-chains 132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13019 Z= 0.266 Angle : 0.613 7.405 18804 Z= 0.373 Chirality : 0.037 0.153 2129 Planarity : 0.004 0.040 1375 Dihedral : 31.281 179.079 4095 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.68 % Allowed : 11.60 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.29), residues: 771 helix: 2.49 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.59 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.002 PHE A 67 TYR 0.010 0.002 TYR H 37 ARG 0.013 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.033 Fit side-chains REVERT: A 53 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7465 (ttp-110) REVERT: A 59 GLU cc_start: 0.7812 (pm20) cc_final: 0.7600 (pm20) REVERT: B 91 LYS cc_start: 0.7657 (tttp) cc_final: 0.7443 (ttmm) REVERT: C 90 ASP cc_start: 0.7286 (t0) cc_final: 0.7047 (t70) REVERT: C 91 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7401 (mp0) REVERT: D 48 ASP cc_start: 0.8608 (m-30) cc_final: 0.8263 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7570 (mtm180) cc_final: 0.7293 (mtm-85) REVERT: E 68 GLN cc_start: 0.7487 (tt0) cc_final: 0.7124 (tt0) REVERT: E 133 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6932 (mt-10) REVERT: F 93 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7031 (mp10) REVERT: G 15 LYS cc_start: 0.7846 (mtmm) cc_final: 0.7340 (mtpt) REVERT: G 90 ASP cc_start: 0.7231 (t0) cc_final: 0.6976 (t0) REVERT: G 95 LYS cc_start: 0.8039 (tttt) cc_final: 0.7674 (tppt) REVERT: G 99 ARG cc_start: 0.7592 (mmm160) cc_final: 0.7173 (mpt180) REVERT: H 31 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7731 (mttp) REVERT: H 105 LYS cc_start: 0.7431 (ttpt) cc_final: 0.6990 (mmtm) outliers start: 11 outliers final: 8 residues processed: 128 average time/residue: 2.0785 time to fit residues: 280.1370 Evaluate side-chains 132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13019 Z= 0.257 Angle : 0.607 7.369 18804 Z= 0.369 Chirality : 0.036 0.153 2129 Planarity : 0.004 0.039 1375 Dihedral : 31.250 179.117 4095 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.14 % Allowed : 11.45 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.29), residues: 771 helix: 2.52 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.57 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.002 PHE A 78 TYR 0.011 0.001 TYR E 54 ARG 0.004 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.006 Fit side-chains REVERT: A 53 ARG cc_start: 0.7837 (ttt180) cc_final: 0.7465 (ttp-110) REVERT: A 59 GLU cc_start: 0.7817 (pm20) cc_final: 0.7607 (pm20) REVERT: B 91 LYS cc_start: 0.7657 (tttp) cc_final: 0.7445 (ttmm) REVERT: C 90 ASP cc_start: 0.7285 (t0) cc_final: 0.7049 (t70) REVERT: C 91 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7401 (mp0) REVERT: D 48 ASP cc_start: 0.8606 (m-30) cc_final: 0.8262 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7576 (mtm180) cc_final: 0.7297 (mtm-85) REVERT: E 68 GLN cc_start: 0.7497 (tt0) cc_final: 0.7129 (tt0) REVERT: E 133 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: F 93 GLN cc_start: 0.7381 (mm-40) cc_final: 0.7023 (mp10) REVERT: G 15 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7293 (mtpt) REVERT: G 90 ASP cc_start: 0.7218 (t0) cc_final: 0.6957 (t0) REVERT: G 95 LYS cc_start: 0.8051 (tttt) cc_final: 0.7684 (tppt) REVERT: G 99 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7173 (mpt180) REVERT: H 31 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7724 (mttp) REVERT: H 105 LYS cc_start: 0.7428 (ttpt) cc_final: 0.6984 (mmtm) outliers start: 14 outliers final: 10 residues processed: 127 average time/residue: 2.0436 time to fit residues: 273.2790 Evaluate side-chains 132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 40.0000 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13019 Z= 0.192 Angle : 0.598 9.543 18804 Z= 0.364 Chirality : 0.035 0.155 2129 Planarity : 0.004 0.038 1375 Dihedral : 31.223 179.123 4095 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.29 % Allowed : 10.99 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.29), residues: 771 helix: 2.59 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.55 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.011 0.001 TYR H 37 ARG 0.014 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.282 Fit side-chains REVERT: A 53 ARG cc_start: 0.7831 (ttt180) cc_final: 0.7462 (ttp-110) REVERT: A 59 GLU cc_start: 0.7807 (pm20) cc_final: 0.7595 (pm20) REVERT: B 91 LYS cc_start: 0.7668 (tttp) cc_final: 0.7450 (ttmm) REVERT: C 90 ASP cc_start: 0.7285 (t0) cc_final: 0.7054 (t70) REVERT: C 91 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7398 (mp0) REVERT: D 48 ASP cc_start: 0.8606 (m-30) cc_final: 0.8267 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7555 (mtm180) cc_final: 0.7281 (mtm-85) REVERT: E 68 GLN cc_start: 0.7482 (tt0) cc_final: 0.7116 (tt0) REVERT: E 133 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6899 (mt-10) REVERT: F 93 GLN cc_start: 0.7378 (mm-40) cc_final: 0.7020 (mp10) REVERT: G 15 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7338 (mtpt) REVERT: G 90 ASP cc_start: 0.7200 (t0) cc_final: 0.6957 (t0) REVERT: G 95 LYS cc_start: 0.8046 (tttt) cc_final: 0.7676 (tppt) REVERT: G 99 ARG cc_start: 0.7589 (mmm160) cc_final: 0.7163 (mpt180) REVERT: H 31 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7724 (mttp) REVERT: H 105 LYS cc_start: 0.7389 (ttpt) cc_final: 0.6952 (mmtm) outliers start: 15 outliers final: 10 residues processed: 129 average time/residue: 2.1127 time to fit residues: 286.7076 Evaluate side-chains 132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 9 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13019 Z= 0.380 Angle : 0.624 6.816 18804 Z= 0.376 Chirality : 0.039 0.157 2129 Planarity : 0.005 0.036 1375 Dihedral : 31.139 178.609 4095 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.83 % Allowed : 11.45 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.29), residues: 771 helix: 2.50 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.63 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.011 0.002 PHE A 104 TYR 0.012 0.002 TYR E 54 ARG 0.006 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.969 Fit side-chains REVERT: A 53 ARG cc_start: 0.7873 (ttt180) cc_final: 0.7474 (ttp-110) REVERT: A 59 GLU cc_start: 0.7848 (pm20) cc_final: 0.7623 (pm20) REVERT: B 91 LYS cc_start: 0.7655 (tttp) cc_final: 0.7156 (ttpt) REVERT: C 90 ASP cc_start: 0.7285 (t0) cc_final: 0.7049 (t70) REVERT: C 91 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7414 (mp0) REVERT: D 48 ASP cc_start: 0.8605 (m-30) cc_final: 0.8264 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7586 (mtm180) cc_final: 0.7310 (mtm-85) REVERT: E 133 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: F 93 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7041 (mp10) REVERT: G 15 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7324 (mtpt) REVERT: G 90 ASP cc_start: 0.7244 (t0) cc_final: 0.7018 (t0) REVERT: G 95 LYS cc_start: 0.8028 (tttt) cc_final: 0.7660 (tppt) REVERT: G 99 ARG cc_start: 0.7586 (mmm160) cc_final: 0.7169 (mpt180) REVERT: H 31 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7846 (mttp) REVERT: H 105 LYS cc_start: 0.7435 (ttpt) cc_final: 0.6983 (mmtm) outliers start: 12 outliers final: 9 residues processed: 126 average time/residue: 2.1123 time to fit residues: 279.8440 Evaluate side-chains 130 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 67 optimal weight: 1.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13019 Z= 0.266 Angle : 0.611 7.086 18804 Z= 0.370 Chirality : 0.036 0.155 2129 Planarity : 0.004 0.037 1375 Dihedral : 31.143 178.758 4095 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.53 % Allowed : 12.06 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.29), residues: 771 helix: 2.54 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.62 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.002 PHE A 104 TYR 0.011 0.002 TYR H 37 ARG 0.010 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.011 Fit side-chains REVERT: A 53 ARG cc_start: 0.7871 (ttt180) cc_final: 0.7476 (ttp-110) REVERT: A 59 GLU cc_start: 0.7855 (pm20) cc_final: 0.7649 (pm20) REVERT: B 91 LYS cc_start: 0.7660 (tttp) cc_final: 0.7441 (ttmm) REVERT: C 73 ASN cc_start: 0.6693 (m-40) cc_final: 0.6370 (t0) REVERT: C 90 ASP cc_start: 0.7284 (t0) cc_final: 0.7050 (t70) REVERT: C 91 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7412 (mp0) REVERT: D 48 ASP cc_start: 0.8609 (m-30) cc_final: 0.8267 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7580 (mtm180) cc_final: 0.7301 (mtm-85) REVERT: E 68 GLN cc_start: 0.7497 (tt0) cc_final: 0.7129 (tt0) REVERT: E 133 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6866 (mt-10) REVERT: F 93 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7033 (mp10) REVERT: G 15 LYS cc_start: 0.7787 (mtmm) cc_final: 0.7264 (mtpt) REVERT: G 90 ASP cc_start: 0.7243 (t0) cc_final: 0.7004 (t0) REVERT: G 95 LYS cc_start: 0.7997 (tttt) cc_final: 0.7626 (tppt) REVERT: G 99 ARG cc_start: 0.7582 (mmm160) cc_final: 0.7164 (mpt180) REVERT: H 31 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7858 (mttp) REVERT: H 105 LYS cc_start: 0.7426 (ttpt) cc_final: 0.6977 (mmtm) outliers start: 10 outliers final: 10 residues processed: 127 average time/residue: 2.0791 time to fit residues: 278.1692 Evaluate side-chains 132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13019 Z= 0.385 Angle : 0.628 6.950 18804 Z= 0.378 Chirality : 0.039 0.157 2129 Planarity : 0.005 0.037 1375 Dihedral : 31.158 178.463 4095 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.37 % Allowed : 12.37 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.29), residues: 771 helix: 2.48 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.011 0.002 PHE A 104 TYR 0.012 0.002 TYR E 54 ARG 0.008 0.000 ARG D 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 1.025 Fit side-chains REVERT: A 53 ARG cc_start: 0.7877 (ttt180) cc_final: 0.7483 (ttp-110) REVERT: A 59 GLU cc_start: 0.7860 (pm20) cc_final: 0.7637 (pm20) REVERT: B 91 LYS cc_start: 0.7633 (tttp) cc_final: 0.7419 (ttmm) REVERT: C 73 ASN cc_start: 0.6751 (m-40) cc_final: 0.6422 (t0) REVERT: C 90 ASP cc_start: 0.7287 (t0) cc_final: 0.7045 (t70) REVERT: C 91 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7411 (mp0) REVERT: D 48 ASP cc_start: 0.8606 (m-30) cc_final: 0.8274 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7584 (mtm180) cc_final: 0.7309 (mtm-85) REVERT: E 133 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6879 (mt-10) REVERT: F 93 GLN cc_start: 0.7399 (mm-40) cc_final: 0.7048 (mp10) REVERT: G 15 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7318 (mtpt) REVERT: G 90 ASP cc_start: 0.7236 (t0) cc_final: 0.7000 (t0) REVERT: G 95 LYS cc_start: 0.7999 (tttt) cc_final: 0.7630 (tppt) REVERT: G 99 ARG cc_start: 0.7592 (mmm160) cc_final: 0.7183 (mpt180) REVERT: H 31 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7899 (mttp) REVERT: H 105 LYS cc_start: 0.7440 (ttpt) cc_final: 0.6981 (mmtm) outliers start: 9 outliers final: 9 residues processed: 126 average time/residue: 2.1192 time to fit residues: 281.1257 Evaluate side-chains 130 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.071023 restraints weight = 22208.032| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.26 r_work: 0.3006 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13019 Z= 0.267 Angle : 0.613 7.087 18804 Z= 0.370 Chirality : 0.036 0.153 2129 Planarity : 0.004 0.037 1375 Dihedral : 31.159 178.689 4095 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.98 % Allowed : 11.91 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.29), residues: 771 helix: 2.53 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.64 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.002 PHE A 104 TYR 0.011 0.002 TYR H 37 ARG 0.009 0.000 ARG D 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4744.72 seconds wall clock time: 85 minutes 22.07 seconds (5122.07 seconds total)