Starting phenix.real_space_refine on Thu Feb 5 16:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mls_48379/02_2026/9mls_48379.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mls_48379/02_2026/9mls_48379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mls_48379/02_2026/9mls_48379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mls_48379/02_2026/9mls_48379.map" model { file = "/net/cci-nas-00/data/ceres_data/9mls_48379/02_2026/9mls_48379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mls_48379/02_2026/9mls_48379.cif" } resolution = 3.6 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= 0.001 sd= 0.012 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 214 5.49 5 S 14 5.16 5 C 5689 2.51 5 N 1890 2.21 5 O 2297 1.98 5 H 8421 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s 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: 18525 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1585 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} 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: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1517 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "D" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1460 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1495 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "F" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1271 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1691 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1436 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 3377 Classifications: {'DNA': 107} Link IDs: {'rna3p': 106} Chain: "J" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 3410 Classifications: {'DNA': 107} Link IDs: {'rna3p': 106} Time building chain proxies: 3.44, per 1000 atoms: 0.19 Number of scatterers: 18525 At special positions: 0 Unit cell: (79.98, 118.68, 116.96, 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 14 16.00 P 214 15.00 O 2297 8.00 N 1890 7.00 C 5689 6.00 H 8421 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: 1.99 Conformation dependent library (CDL) restraints added in 435.4 milliseconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1346 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 75.0% alpha, 2.5% beta 107 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.559A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.784A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.565A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.579A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) 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: 3.570A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.611A 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 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.346A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.782A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 4.093A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.693A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.772A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.845A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.611A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) 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: 4.160A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.505A 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 removed outlier: 3.667A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.701A pdb=" N TYR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.809A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.658A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.906A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.959A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.425A 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 removed outlier: 4.034A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.246A 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: 7.108A 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 'G' and resid 42 through 43 removed outlier: 7.005A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.648A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 373 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 275 hydrogen bonds 550 hydrogen bond angles 0 basepair planarities 107 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 8417 1.03 - 1.22: 51 1.22 - 1.42: 4510 1.42 - 1.61: 6130 1.61 - 1.81: 24 Bond restraints: 19132 Sorted by residual: bond pdb=" CG GLU G 92 " pdb=" CD GLU G 92 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.97e+00 bond pdb=" CG1 ILE D 51 " pdb=" CD1 ILE D 51 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.75e+00 bond pdb=" C4' DG J -8 " pdb=" O4' DG J -8 " ideal model delta sigma weight residual 1.450 1.421 0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C4' DC I 37 " pdb=" O4' DC I 37 " ideal model delta sigma weight residual 1.450 1.421 0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" CG LEU D 77 " pdb=" CD1 LEU D 77 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 ... (remaining 19127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 33319 1.98 - 3.96: 1302 3.96 - 5.93: 45 5.93 - 7.91: 2 7.91 - 9.89: 1 Bond angle restraints: 34669 Sorted by residual: angle pdb=" CB ARG E 63 " pdb=" CG ARG E 63 " pdb=" CD ARG E 63 " ideal model delta sigma weight residual 111.30 121.19 -9.89 2.30e+00 1.89e-01 1.85e+01 angle pdb=" CA GLN F 27 " pdb=" CB GLN F 27 " pdb=" CG GLN F 27 " ideal model delta sigma weight residual 114.10 120.76 -6.66 2.00e+00 2.50e-01 1.11e+01 angle pdb=" N ILE D 51 " pdb=" CA ILE D 51 " pdb=" C ILE D 51 " ideal model delta sigma weight residual 108.45 113.37 -4.92 1.48e+00 4.57e-01 1.11e+01 angle pdb=" C4' DC I 21 " pdb=" O4' DC I 21 " pdb=" C1' DC I 21 " ideal model delta sigma weight residual 109.70 104.75 4.95 1.50e+00 4.44e-01 1.09e+01 angle pdb=" C2' DT I -26 " pdb=" C1' DT I -26 " pdb=" N1 DT I -26 " ideal model delta sigma weight residual 113.50 118.44 -4.94 1.50e+00 4.44e-01 1.08e+01 ... (remaining 34664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5880 17.95 - 35.90: 1009 35.90 - 53.85: 764 53.85 - 71.80: 373 71.80 - 89.75: 21 Dihedral angle restraints: 8047 sinusoidal: 5702 harmonic: 2345 Sorted by residual: dihedral pdb=" CA SER D 84 " pdb=" C SER D 84 " pdb=" N THR D 85 " pdb=" CA THR D 85 " ideal model delta harmonic sigma weight residual -180.00 -155.95 -24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA THR H 85 " pdb=" C THR H 85 " pdb=" N ILE H 86 " pdb=" CA ILE H 86 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ASP H 48 " pdb=" C ASP H 48 " pdb=" N THR H 49 " pdb=" CA THR H 49 " ideal model delta harmonic sigma weight residual 180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 8044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 989 0.036 - 0.072: 530 0.072 - 0.108: 186 0.108 - 0.144: 41 0.144 - 0.180: 9 Chirality restraints: 1755 Sorted by residual: chirality pdb=" CA TYR E 54 " pdb=" N TYR E 54 " pdb=" C TYR E 54 " pdb=" CB TYR E 54 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CA GLN C 104 " pdb=" N GLN C 104 " pdb=" C GLN C 104 " pdb=" CB GLN C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" C1' DG I 54 " pdb=" O4' DG I 54 " pdb=" C2' DG I 54 " pdb=" N9 DG I 54 " both_signs ideal model delta sigma weight residual False 2.42 2.25 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1752 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 78 " 0.258 9.50e-02 1.11e+02 9.17e-02 3.03e+01 pdb=" NE ARG B 78 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 78 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 78 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 78 " -0.067 2.00e-02 2.50e+03 pdb="HH11 ARG B 78 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 78 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG B 78 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG B 78 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 83 " 0.329 9.50e-02 1.11e+02 1.13e-01 2.85e+01 pdb=" NE ARG H 83 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG H 83 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG H 83 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG H 83 " -0.044 2.00e-02 2.50e+03 pdb="HH11 ARG H 83 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG H 83 " 0.026 2.00e-02 2.50e+03 pdb="HH21 ARG H 83 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 83 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 83 " 0.280 9.50e-02 1.11e+02 9.64e-02 2.15e+01 pdb=" NE ARG E 83 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG E 83 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 83 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG E 83 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG E 83 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 83 " 0.009 2.00e-02 2.50e+03 pdb="HH21 ARG E 83 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 83 " 0.047 2.00e-02 2.50e+03 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 232 2.06 - 2.70: 24881 2.70 - 3.33: 48595 3.33 - 3.97: 64046 3.97 - 4.60: 101422 Nonbonded interactions: 239176 Sorted by model distance: nonbonded pdb=" OE1 GLU C 41 " pdb=" H GLU C 41 " model vdw 1.426 2.450 nonbonded pdb="HH22 ARG G 32 " pdb=" OE1 GLU H 32 " model vdw 1.530 2.450 nonbonded pdb=" OE1 GLU G 41 " pdb=" H GLU G 41 " model vdw 1.555 2.450 nonbonded pdb=" HG SER D 84 " pdb=" OP1 DG I -34 " model vdw 1.564 2.450 nonbonded pdb=" HZ2 LYS B 44 " pdb=" O LEU G 115 " model vdw 1.565 2.450 ... (remaining 239171 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 45 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 13 through 108) } ncs_group { reference = (chain 'D' and resid 31 through 121) 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: 3.450 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: 0.080 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 21.590 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.005 0.065 10711 Z= 0.233 Angle : 0.894 9.889 15370 Z= 0.562 Chirality : 0.048 0.180 1755 Planarity : 0.012 0.120 1202 Dihedral : 26.247 89.753 4549 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.17 % Allowed : 12.06 % Favored : 87.77 % 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: -0.37 (0.28), residues: 708 helix: 0.02 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -0.62 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG G 20 TYR 0.022 0.004 TYR F 98 PHE 0.017 0.002 PHE A 78 HIS 0.007 0.003 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00501 (10711) covalent geometry : angle 0.89420 (15370) hydrogen bonds : bond 0.10281 ( 648) hydrogen bonds : angle 4.17976 ( 1648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.414 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: A 74 ILE cc_start: 0.9218 (mt) cc_final: 0.8966 (mt) REVERT: E 59 GLU cc_start: 0.7437 (pm20) cc_final: 0.6937 (pm20) outliers start: 1 outliers final: 1 residues processed: 230 average time/residue: 0.3339 time to fit residues: 96.0975 Evaluate side-chains 161 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 93 GLN B 93 GLN C 73 ASN C 94 ASN D 64 ASN D 92 GLN D 106 HIS E 68 GLN E 108 ASN F 25 ASN G 68 ASN G 89 ASN H 79 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.060919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046450 restraints weight = 124336.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048298 restraints weight = 49790.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049569 restraints weight = 29670.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.050354 restraints weight = 21959.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050886 restraints weight = 18537.993| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10711 Z= 0.232 Angle : 0.680 5.621 15370 Z= 0.419 Chirality : 0.042 0.135 1755 Planarity : 0.005 0.056 1202 Dihedral : 28.737 97.419 3142 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.51 % Allowed : 17.76 % Favored : 79.73 % 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: 1.53 (0.30), residues: 708 helix: 1.67 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -0.87 (0.39), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 78 TYR 0.013 0.001 TYR C 39 PHE 0.009 0.001 PHE A 78 HIS 0.005 0.002 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00487 (10711) covalent geometry : angle 0.67996 (15370) hydrogen bonds : bond 0.06005 ( 648) hydrogen bonds : angle 3.72052 ( 1648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.421 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: B 43 VAL cc_start: 0.9269 (t) cc_final: 0.8972 (p) REVERT: B 63 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7811 (mt-10) REVERT: B 84 MET cc_start: 0.7945 (mpp) cc_final: 0.7730 (mmt) REVERT: C 92 GLU cc_start: 0.8704 (pm20) cc_final: 0.8256 (pm20) REVERT: D 73 GLU cc_start: 0.8796 (tp30) cc_final: 0.8357 (tp30) REVERT: E 59 GLU cc_start: 0.7271 (pm20) cc_final: 0.6978 (pm20) REVERT: E 60 LEU cc_start: 0.8489 (mp) cc_final: 0.8210 (mp) REVERT: H 31 LYS cc_start: 0.8045 (mptt) cc_final: 0.7656 (mmmm) REVERT: H 90 GLU cc_start: 0.8963 (mp0) cc_final: 0.8186 (mp0) outliers start: 15 outliers final: 10 residues processed: 176 average time/residue: 0.2916 time to fit residues: 65.9589 Evaluate side-chains 164 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.060086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.045419 restraints weight = 125393.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.047217 restraints weight = 50854.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.048431 restraints weight = 30482.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049220 restraints weight = 22759.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.049678 restraints weight = 19262.637| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10711 Z= 0.212 Angle : 0.644 5.681 15370 Z= 0.399 Chirality : 0.041 0.131 1755 Planarity : 0.005 0.035 1202 Dihedral : 28.742 90.646 3138 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.18 % Allowed : 20.10 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.95 (0.31), residues: 708 helix: 2.06 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.01 (0.39), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 78 TYR 0.010 0.001 TYR C 39 PHE 0.007 0.001 PHE B 61 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00444 (10711) covalent geometry : angle 0.64391 (15370) hydrogen bonds : bond 0.05380 ( 648) hydrogen bonds : angle 3.60781 ( 1648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.406 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: B 43 VAL cc_start: 0.9416 (t) cc_final: 0.9156 (p) REVERT: B 63 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7848 (mt-10) REVERT: B 84 MET cc_start: 0.7996 (mpp) cc_final: 0.7695 (mmt) REVERT: D 48 ASP cc_start: 0.9028 (m-30) cc_final: 0.8624 (p0) REVERT: D 54 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8643 (mmmm) REVERT: D 73 GLU cc_start: 0.8810 (tp30) cc_final: 0.8535 (tp30) REVERT: E 60 LEU cc_start: 0.8691 (mp) cc_final: 0.8301 (mp) REVERT: H 90 GLU cc_start: 0.9055 (mp0) cc_final: 0.8386 (mp0) outliers start: 19 outliers final: 13 residues processed: 168 average time/residue: 0.2900 time to fit residues: 62.7514 Evaluate side-chains 157 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 22 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.059693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.045077 restraints weight = 126408.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046867 restraints weight = 51162.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.048095 restraints weight = 30733.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.048866 restraints weight = 22945.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.049320 restraints weight = 19450.396| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10711 Z= 0.197 Angle : 0.634 8.501 15370 Z= 0.391 Chirality : 0.040 0.131 1755 Planarity : 0.004 0.034 1202 Dihedral : 28.829 90.710 3138 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.52 % Allowed : 20.10 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.31), residues: 708 helix: 2.18 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.09 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 69 TYR 0.007 0.001 TYR D 39 PHE 0.010 0.001 PHE A 84 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00414 (10711) covalent geometry : angle 0.63419 (15370) hydrogen bonds : bond 0.05166 ( 648) hydrogen bonds : angle 3.52571 ( 1648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.409 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: A 59 GLU cc_start: 0.8346 (tp30) cc_final: 0.8029 (tp30) REVERT: A 68 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.8697 (tm130) REVERT: B 63 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 84 MET cc_start: 0.8059 (mpp) cc_final: 0.7770 (mmt) REVERT: C 90 ASP cc_start: 0.8511 (m-30) cc_final: 0.8022 (t70) REVERT: C 92 GLU cc_start: 0.8246 (pm20) cc_final: 0.7411 (pm20) REVERT: D 54 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8588 (mmmm) REVERT: D 65 ASP cc_start: 0.9306 (t0) cc_final: 0.9095 (t70) REVERT: D 96 ARG cc_start: 0.8828 (mtm110) cc_final: 0.8522 (ttm110) REVERT: E 60 LEU cc_start: 0.8694 (mp) cc_final: 0.8318 (mp) REVERT: F 88 TYR cc_start: 0.9269 (m-10) cc_final: 0.8874 (m-10) REVERT: G 56 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8523 (tm-30) REVERT: H 75 SER cc_start: 0.9590 (t) cc_final: 0.9356 (p) REVERT: H 90 GLU cc_start: 0.9083 (mp0) cc_final: 0.8423 (mp0) outliers start: 21 outliers final: 16 residues processed: 169 average time/residue: 0.2835 time to fit residues: 62.0306 Evaluate side-chains 160 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.058740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.044253 restraints weight = 125101.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.046006 restraints weight = 50755.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.047198 restraints weight = 30525.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047941 restraints weight = 22797.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.048382 restraints weight = 19290.107| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10711 Z= 0.222 Angle : 0.634 6.694 15370 Z= 0.392 Chirality : 0.041 0.128 1755 Planarity : 0.004 0.035 1202 Dihedral : 28.899 88.405 3138 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.52 % Allowed : 21.61 % Favored : 74.87 % 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: 1.98 (0.31), residues: 708 helix: 2.16 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.25 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 83 TYR 0.018 0.002 TYR H 80 PHE 0.008 0.001 PHE A 84 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00466 (10711) covalent geometry : angle 0.63398 (15370) hydrogen bonds : bond 0.05574 ( 648) hydrogen bonds : angle 3.65014 ( 1648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.412 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: A 59 GLU cc_start: 0.8347 (tp30) cc_final: 0.8039 (tp30) REVERT: A 68 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.8713 (tm130) REVERT: B 63 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7890 (mt-10) REVERT: B 84 MET cc_start: 0.8088 (mpp) cc_final: 0.7801 (mmt) REVERT: C 73 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.8984 (t0) REVERT: C 90 ASP cc_start: 0.8624 (m-30) cc_final: 0.8217 (t70) REVERT: C 92 GLU cc_start: 0.8345 (pm20) cc_final: 0.7484 (pm20) REVERT: D 54 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8520 (mmmm) REVERT: D 96 ARG cc_start: 0.8850 (mtm110) cc_final: 0.8501 (ttm110) REVERT: G 56 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8513 (tm-30) REVERT: H 75 SER cc_start: 0.9527 (t) cc_final: 0.9283 (p) REVERT: H 90 GLU cc_start: 0.9119 (mp0) cc_final: 0.8347 (mp0) outliers start: 21 outliers final: 17 residues processed: 164 average time/residue: 0.2867 time to fit residues: 60.9420 Evaluate side-chains 159 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 35 optimal weight: 0.0970 chunk 57 optimal weight: 0.0870 chunk 4 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 1.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.059393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.044726 restraints weight = 125289.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.046479 restraints weight = 50732.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.047689 restraints weight = 30434.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.048347 restraints weight = 22744.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.048859 restraints weight = 19608.524| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10711 Z= 0.179 Angle : 0.616 7.052 15370 Z= 0.380 Chirality : 0.039 0.135 1755 Planarity : 0.004 0.035 1202 Dihedral : 28.939 89.373 3138 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.02 % Allowed : 21.27 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.31), residues: 708 helix: 2.40 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.26 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 83 TYR 0.016 0.001 TYR F 88 PHE 0.009 0.001 PHE A 84 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00372 (10711) covalent geometry : angle 0.61610 (15370) hydrogen bonds : bond 0.04855 ( 648) hydrogen bonds : angle 3.39881 ( 1648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.267 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: A 59 GLU cc_start: 0.8372 (tp30) cc_final: 0.8055 (tp30) REVERT: A 64 LYS cc_start: 0.8216 (mtmm) cc_final: 0.7971 (mtmm) REVERT: A 68 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8687 (tm130) REVERT: B 63 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 84 MET cc_start: 0.8048 (mpp) cc_final: 0.7729 (mmt) REVERT: C 73 ASN cc_start: 0.9404 (OUTLIER) cc_final: 0.9015 (t0) REVERT: C 90 ASP cc_start: 0.8620 (m-30) cc_final: 0.8274 (t70) REVERT: C 92 GLU cc_start: 0.8410 (pm20) cc_final: 0.7558 (pm20) REVERT: D 54 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8456 (mmmm) REVERT: D 96 ARG cc_start: 0.8853 (mtm110) cc_final: 0.8491 (ttm110) REVERT: H 75 SER cc_start: 0.9460 (t) cc_final: 0.9202 (p) REVERT: H 90 GLU cc_start: 0.9109 (mp0) cc_final: 0.8510 (mp0) outliers start: 18 outliers final: 15 residues processed: 171 average time/residue: 0.2876 time to fit residues: 63.5288 Evaluate side-chains 165 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.060368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045833 restraints weight = 125135.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.047655 restraints weight = 50571.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.048906 restraints weight = 30232.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049685 restraints weight = 22477.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.050157 restraints weight = 18952.351| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10711 Z= 0.161 Angle : 0.615 7.452 15370 Z= 0.377 Chirality : 0.038 0.177 1755 Planarity : 0.004 0.035 1202 Dihedral : 28.938 89.136 3138 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.51 % Allowed : 23.28 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.31), residues: 708 helix: 2.63 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.17 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 83 TYR 0.018 0.001 TYR F 88 PHE 0.008 0.001 PHE A 84 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00342 (10711) covalent geometry : angle 0.61515 (15370) hydrogen bonds : bond 0.04375 ( 648) hydrogen bonds : angle 3.14943 ( 1648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.408 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: A 59 GLU cc_start: 0.8361 (tp30) cc_final: 0.8036 (tp30) REVERT: A 64 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7939 (mtmm) REVERT: A 68 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.8730 (tm130) REVERT: A 79 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8583 (ttpp) REVERT: B 63 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7813 (mt-10) REVERT: B 84 MET cc_start: 0.8076 (mpp) cc_final: 0.7736 (mmt) REVERT: C 90 ASP cc_start: 0.8594 (m-30) cc_final: 0.8293 (t70) REVERT: C 92 GLU cc_start: 0.8414 (pm20) cc_final: 0.7562 (pm20) REVERT: D 96 ARG cc_start: 0.8842 (mtm110) cc_final: 0.8484 (ttm110) REVERT: G 90 ASP cc_start: 0.8852 (t0) cc_final: 0.8282 (t0) REVERT: H 31 LYS cc_start: 0.8440 (mptt) cc_final: 0.8240 (mmtm) REVERT: H 90 GLU cc_start: 0.9083 (mp0) cc_final: 0.8480 (mp0) outliers start: 15 outliers final: 13 residues processed: 167 average time/residue: 0.2898 time to fit residues: 62.3578 Evaluate side-chains 162 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.043830 restraints weight = 126774.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.045546 restraints weight = 51790.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.046736 restraints weight = 31262.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047463 restraints weight = 23389.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047897 restraints weight = 19845.183| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10711 Z= 0.249 Angle : 0.642 6.141 15370 Z= 0.396 Chirality : 0.042 0.131 1755 Planarity : 0.004 0.035 1202 Dihedral : 28.992 89.462 3138 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.35 % Allowed : 22.61 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.31), residues: 708 helix: 2.32 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.43 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 83 TYR 0.013 0.002 TYR F 88 PHE 0.011 0.001 PHE A 84 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00528 (10711) covalent geometry : angle 0.64192 (15370) hydrogen bonds : bond 0.05738 ( 648) hydrogen bonds : angle 3.68254 ( 1648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.457 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: A 59 GLU cc_start: 0.8371 (tp30) cc_final: 0.8064 (tp30) REVERT: A 64 LYS cc_start: 0.8301 (mtmm) cc_final: 0.8028 (mtmm) REVERT: A 68 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.8787 (tm130) REVERT: B 63 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 84 MET cc_start: 0.8098 (mpp) cc_final: 0.7762 (mmt) REVERT: D 54 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8494 (mmmm) REVERT: D 96 ARG cc_start: 0.8873 (mtm110) cc_final: 0.8476 (ttm110) REVERT: F 93 GLN cc_start: 0.9197 (tt0) cc_final: 0.8905 (tm-30) REVERT: G 56 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8571 (tm-30) REVERT: G 90 ASP cc_start: 0.8875 (t0) cc_final: 0.8325 (t0) REVERT: H 75 SER cc_start: 0.9426 (t) cc_final: 0.9180 (p) REVERT: H 90 GLU cc_start: 0.9136 (mp0) cc_final: 0.8367 (mp0) outliers start: 20 outliers final: 18 residues processed: 157 average time/residue: 0.2868 time to fit residues: 58.4493 Evaluate side-chains 154 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 58 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 0.0040 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.5130 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.060622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.046486 restraints weight = 124154.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.048347 restraints weight = 49071.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049605 restraints weight = 28818.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.050391 restraints weight = 21175.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050853 restraints weight = 17713.883| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10711 Z= 0.158 Angle : 0.618 7.155 15370 Z= 0.377 Chirality : 0.037 0.144 1755 Planarity : 0.004 0.037 1202 Dihedral : 28.941 89.328 3138 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.51 % Allowed : 24.12 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.32), residues: 708 helix: 2.75 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.31 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 76 TYR 0.026 0.001 TYR F 88 PHE 0.006 0.001 PHE D 62 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00344 (10711) covalent geometry : angle 0.61771 (15370) hydrogen bonds : bond 0.03986 ( 648) hydrogen bonds : angle 3.07095 ( 1648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.495 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: A 59 GLU cc_start: 0.8358 (tp30) cc_final: 0.8037 (tp30) REVERT: A 64 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7998 (mtmm) REVERT: A 79 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8601 (ttpp) REVERT: B 84 MET cc_start: 0.8050 (mpp) cc_final: 0.7694 (mmt) REVERT: C 90 ASP cc_start: 0.8528 (m-30) cc_final: 0.8244 (t70) REVERT: C 92 GLU cc_start: 0.8357 (pm20) cc_final: 0.7760 (pm20) REVERT: F 93 GLN cc_start: 0.9191 (tt0) cc_final: 0.8912 (tm-30) REVERT: H 90 GLU cc_start: 0.9095 (mp0) cc_final: 0.8514 (mp0) outliers start: 15 outliers final: 10 residues processed: 161 average time/residue: 0.2893 time to fit residues: 60.4271 Evaluate side-chains 155 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.059827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.045684 restraints weight = 124526.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.047501 restraints weight = 49896.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.048736 restraints weight = 29570.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049509 restraints weight = 21844.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049997 restraints weight = 18341.368| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10711 Z= 0.175 Angle : 0.621 6.459 15370 Z= 0.380 Chirality : 0.038 0.136 1755 Planarity : 0.004 0.057 1202 Dihedral : 28.937 89.978 3138 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.51 % Allowed : 24.79 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.31), residues: 708 helix: 2.71 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.41 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.016 0.001 TYR F 88 PHE 0.007 0.001 PHE A 84 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00372 (10711) covalent geometry : angle 0.62143 (15370) hydrogen bonds : bond 0.04598 ( 648) hydrogen bonds : angle 3.20179 ( 1648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.467 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: A 59 GLU cc_start: 0.8348 (tp30) cc_final: 0.8032 (tp30) REVERT: A 64 LYS cc_start: 0.8294 (mtmm) cc_final: 0.8000 (mtmm) REVERT: A 79 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8591 (ttpp) REVERT: B 84 MET cc_start: 0.8050 (mpp) cc_final: 0.7645 (mmt) REVERT: C 90 ASP cc_start: 0.8444 (m-30) cc_final: 0.8058 (t70) REVERT: C 92 GLU cc_start: 0.8325 (pm20) cc_final: 0.7672 (pm20) REVERT: D 54 LYS cc_start: 0.8721 (mmmm) cc_final: 0.8418 (mmmm) REVERT: E 60 LEU cc_start: 0.8812 (mp) cc_final: 0.8526 (mp) REVERT: F 93 GLN cc_start: 0.9174 (tt0) cc_final: 0.8921 (tm-30) REVERT: G 56 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8517 (tm-30) REVERT: G 90 ASP cc_start: 0.8911 (t0) cc_final: 0.8390 (t0) REVERT: H 90 GLU cc_start: 0.9108 (mp0) cc_final: 0.8356 (mp0) outliers start: 9 outliers final: 7 residues processed: 147 average time/residue: 0.2916 time to fit residues: 55.5169 Evaluate side-chains 147 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.060525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.046002 restraints weight = 125548.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047819 restraints weight = 50591.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049078 restraints weight = 30304.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049854 restraints weight = 22566.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.050290 restraints weight = 19059.180| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10711 Z= 0.160 Angle : 0.616 7.517 15370 Z= 0.376 Chirality : 0.037 0.134 1755 Planarity : 0.004 0.038 1202 Dihedral : 28.884 89.926 3138 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.17 % Allowed : 25.80 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.32), residues: 708 helix: 2.85 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.37 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.015 0.001 TYR F 88 PHE 0.006 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00345 (10711) covalent geometry : angle 0.61583 (15370) hydrogen bonds : bond 0.04079 ( 648) hydrogen bonds : angle 3.02724 ( 1648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3406.80 seconds wall clock time: 58 minutes 46.73 seconds (3526.73 seconds total)