Starting phenix.real_space_refine on Thu Jul 2 20:58:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sx6_55332/07_2026/9sx6_55332.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sx6_55332/07_2026/9sx6_55332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sx6_55332/07_2026/9sx6_55332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sx6_55332/07_2026/9sx6_55332.map" model { file = "/net/cci-nas-00/data/ceres_data/9sx6_55332/07_2026/9sx6_55332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sx6_55332/07_2026/9sx6_55332.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 58 5.49 5 S 24 5.16 5 C 6264 2.51 5 N 1735 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10133 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "H" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "C" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "B" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "E" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "D" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "G" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "F" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "Y" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 607 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "Z" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 582 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Time building chain proxies: 2.11, per 1000 atoms: 0.21 Number of scatterers: 10133 At special positions: 0 Unit cell: (56.763, 127.041, 138.754, 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 24 16.00 P 58 15.00 O 2052 8.00 N 1735 7.00 C 6264 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: 0.63 Conformation dependent library (CDL) restraints added in 243.2 milliseconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 16 sheets defined 44.2% alpha, 22.3% beta 28 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 4.029A pdb=" N SER A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.044A pdb=" N GLU A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 75 removed outlier: 4.249A pdb=" N ASN A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.696A pdb=" N MET A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 24 removed outlier: 3.925A pdb=" N SER H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 56 removed outlier: 3.747A pdb=" N GLU H 49 " --> pdb=" O PRO H 45 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 75 removed outlier: 4.244A pdb=" N ASN H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 98 Processing helix chain 'H' and resid 117 through 126 Processing helix chain 'H' and resid 129 through 137 removed outlier: 3.657A pdb=" N MET H 137 " --> pdb=" O VAL H 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 removed outlier: 4.014A pdb=" N SER C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 57 Processing helix chain 'C' and resid 62 through 75 removed outlier: 4.528A pdb=" N ASN C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.993A pdb=" N SER C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.708A pdb=" N GLU B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 75 removed outlier: 4.025A pdb=" N ASN B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'E' and resid 19 through 25 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.829A pdb=" N GLU E 49 " --> pdb=" O PRO E 45 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 75 removed outlier: 4.151A pdb=" N ASN E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 98 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 129 through 137 removed outlier: 3.749A pdb=" N MET E 137 " --> pdb=" O VAL E 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.737A pdb=" N SER D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 57 removed outlier: 3.822A pdb=" N ASN D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 75 removed outlier: 4.104A pdb=" N ASN D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 98 removed outlier: 3.757A pdb=" N ASP D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 129 through 136 removed outlier: 3.535A pdb=" N ARG D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 removed outlier: 4.167A pdb=" N SER G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 57 removed outlier: 3.710A pdb=" N ASN G 57 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 74 Processing helix chain 'G' and resid 90 through 98 removed outlier: 3.813A pdb=" N SER G 95 " --> pdb=" O ASN G 91 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 126 Processing helix chain 'G' and resid 129 through 136 removed outlier: 3.587A pdb=" N ARG G 136 " --> pdb=" O THR G 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 62 through 75 removed outlier: 4.054A pdb=" N ASN F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 98 removed outlier: 3.562A pdb=" N SER F 95 " --> pdb=" O ASN F 91 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'F' and resid 129 through 136 removed outlier: 3.589A pdb=" N ARG F 136 " --> pdb=" O THR F 132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 removed outlier: 3.779A pdb=" N CYS A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'H' and resid 5 through 9 Processing sheet with id=AA4, first strand: chain 'H' and resid 15 through 17 Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.790A pdb=" N HIS C 111 " --> pdb=" O GLN C 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.600A pdb=" N HIS B 111 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 15 through 17 Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 8 removed outlier: 3.973A pdb=" N CYS E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 15 through 17 Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 9 removed outlier: 3.803A pdb=" N CYS D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=AB4, first strand: chain 'G' and resid 3 through 9 removed outlier: 3.851A pdb=" N GLY G 4 " --> pdb=" O GLY G 107 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N CYS G 39 " --> pdb=" O GLY G 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=AB6, first strand: chain 'F' and resid 3 through 8 removed outlier: 3.956A pdb=" N GLY F 4 " --> pdb=" O GLY F 107 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 16 through 17 449 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2610 1.33 - 1.45: 2070 1.45 - 1.57: 5594 1.57 - 1.69: 114 1.69 - 1.80: 40 Bond restraints: 10428 Sorted by residual: bond pdb=" O3' DT Z -6 " pdb=" P DT Z -5 " ideal model delta sigma weight residual 1.607 1.687 -0.080 1.50e-02 4.44e+03 2.81e+01 bond pdb=" C3' DT Z 12 " pdb=" C2' DT Z 12 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DC Z 20 " pdb=" C2' DC Z 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC Z 10 " pdb=" C2' DC Z 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA Z -1 " pdb=" C2' DA Z -1 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.67e+00 ... (remaining 10423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 14258 3.45 - 6.91: 76 6.91 - 10.36: 3 10.36 - 13.82: 0 13.82 - 17.27: 2 Bond angle restraints: 14339 Sorted by residual: angle pdb=" O3' DT Z -6 " pdb=" P DT Z -5 " pdb=" OP2 DT Z -5 " ideal model delta sigma weight residual 108.00 125.27 -17.27 3.00e+00 1.11e-01 3.31e+01 angle pdb=" C3' DT Z -6 " pdb=" O3' DT Z -6 " pdb=" P DT Z -5 " ideal model delta sigma weight residual 120.20 112.41 7.79 1.50e+00 4.44e-01 2.69e+01 angle pdb=" O3' DT Z -6 " pdb=" P DT Z -5 " pdb=" OP1 DT Z -5 " ideal model delta sigma weight residual 108.00 93.47 14.53 3.00e+00 1.11e-01 2.34e+01 angle pdb=" N3 DT Z 12 " pdb=" C4 DT Z 12 " pdb=" O4 DT Z 12 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" O4' DA Y 6 " pdb=" C4' DA Y 6 " pdb=" C3' DA Y 6 " ideal model delta sigma weight residual 106.00 103.38 2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 14334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.75: 5646 31.75 - 63.49: 541 63.49 - 95.24: 20 95.24 - 126.99: 0 126.99 - 158.74: 3 Dihedral angle restraints: 6210 sinusoidal: 2954 harmonic: 3256 Sorted by residual: dihedral pdb=" CA LYS H 13 " pdb=" C LYS H 13 " pdb=" N ASN H 14 " pdb=" CA ASN H 14 " ideal model delta harmonic sigma weight residual 180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LYS F 101 " pdb=" C LYS F 101 " pdb=" N GLU F 102 " pdb=" CA GLU F 102 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA LYS F 13 " pdb=" C LYS F 13 " pdb=" N ASN F 14 " pdb=" CA ASN F 14 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 6207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1580 0.116 - 0.232: 51 0.232 - 0.347: 0 0.347 - 0.463: 0 0.463 - 0.579: 1 Chirality restraints: 1632 Sorted by residual: chirality pdb=" P DA Y 6 " pdb=" OP1 DA Y 6 " pdb=" OP2 DA Y 6 " pdb=" O5' DA Y 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CA ASP D 82 " pdb=" N ASP D 82 " pdb=" C ASP D 82 " pdb=" CB ASP D 82 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C3' DA Y -13 " pdb=" C4' DA Y -13 " pdb=" O3' DA Y -13 " pdb=" C2' DA Y -13 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.65e-01 ... (remaining 1629 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 91 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" CG ASN B 91 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 91 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 91 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 82 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" CG ASP D 82 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP D 82 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP D 82 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 52 " 0.011 2.00e-02 2.50e+03 1.19e-02 2.48e+00 pdb=" CG PHE A 52 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 52 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 52 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 52 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 52 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 52 " 0.001 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 4727 2.96 - 3.45: 10213 3.45 - 3.93: 17035 3.93 - 4.42: 19227 4.42 - 4.90: 30548 Nonbonded interactions: 81750 Sorted by model distance: nonbonded pdb=" O5' DA Z 17 " pdb=" O4' DA Z 17 " model vdw 2.478 2.432 nonbonded pdb=" O5' DG Y 2 " pdb=" O4' DG Y 2 " model vdw 2.483 2.432 nonbonded pdb=" O SER B 126 " pdb=" OG SER B 126 " model vdw 2.486 3.040 nonbonded pdb=" O5' DG Y 3 " pdb=" O4' DG Y 3 " model vdw 2.512 2.432 nonbonded pdb=" O5' DC Z -2 " pdb=" O4' DC Z -2 " model vdw 2.513 2.432 ... (remaining 81745 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.040 Find NCS groups from input model: 0.110 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 0.080 10428 Z= 0.303 Angle : 0.751 17.271 14339 Z= 0.493 Chirality : 0.049 0.579 1632 Planarity : 0.004 0.043 1658 Dihedral : 20.982 158.737 4066 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.59 % Favored : 92.31 % Rotamer: Outliers : 4.17 % Allowed : 27.08 % Favored : 68.75 % 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: -0.39 (0.26), residues: 1080 helix: 0.20 (0.24), residues: 456 sheet: 0.63 (0.27), residues: 384 loop : -2.47 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 15 TYR 0.009 0.001 TYR B 120 PHE 0.027 0.001 PHE A 52 TRP 0.014 0.002 TRP D 115 HIS 0.004 0.002 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.30 (10428) covalent geometry : angle 0.75078 / 0.49 (14339) hydrogen bonds : bond 0.12576 / 8.80 ( 517) hydrogen bonds : angle 5.87953 / 4.11 ( 1423) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 0.395 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: A 30 ILE cc_start: 0.8623 (pp) cc_final: 0.8304 (pt) REVERT: A 32 ILE cc_start: 0.8621 (tp) cc_final: 0.8337 (tt) REVERT: A 87 ILE cc_start: 0.7930 (mt) cc_final: 0.7690 (mt) REVERT: F 51 TYR cc_start: 0.7701 (t80) cc_final: 0.7479 (t80) outliers start: 42 outliers final: 10 residues processed: 272 average time/residue: 0.0897 time to fit residues: 33.9429 Evaluate side-chains 171 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 109 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.0000 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN A 56 ASN A 85 ASN C 33 ASN C 38 ASN C 85 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 77 ASN B 91 ASN E 85 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN D 75 ASN G 85 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.056337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.043060 restraints weight = 44659.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.044422 restraints weight = 21462.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.045357 restraints weight = 13462.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.045976 restraints weight = 9786.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.046309 restraints weight = 7853.069| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10428 Z= 0.219 Angle : 0.693 7.765 14339 Z= 0.392 Chirality : 0.048 0.297 1632 Planarity : 0.004 0.039 1658 Dihedral : 21.505 163.644 1839 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.41 % Favored : 92.22 % Rotamer: Outliers : 5.65 % Allowed : 23.21 % Favored : 71.13 % 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: -0.28 (0.26), residues: 1080 helix: 0.06 (0.24), residues: 464 sheet: 0.91 (0.31), residues: 304 loop : -1.54 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 23 TYR 0.013 0.001 TYR B 120 PHE 0.023 0.002 PHE D 52 TRP 0.013 0.002 TRP H 115 HIS 0.003 0.001 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (10428) covalent geometry : angle 0.69288 / 0.39 (14339) hydrogen bonds : bond 0.05005 / 3.31 ( 517) hydrogen bonds : angle 5.39346 / 3.81 ( 1423) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 0.273 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: A 7 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8314 (t0) REVERT: A 51 TYR cc_start: 0.9184 (t80) cc_final: 0.8971 (t80) REVERT: A 118 VAL cc_start: 0.9407 (t) cc_final: 0.8986 (p) REVERT: C 33 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8139 (p0) REVERT: C 49 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 53 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8392 (mm110) REVERT: B 49 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 95 SER cc_start: 0.8970 (t) cc_final: 0.8701 (p) REVERT: B 122 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8625 (tp-100) REVERT: E 88 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7906 (pp) REVERT: D 49 GLU cc_start: 0.8716 (tp30) cc_final: 0.8422 (tp30) REVERT: D 98 LYS cc_start: 0.9207 (mtpp) cc_final: 0.8862 (mtmm) REVERT: G 49 GLU cc_start: 0.8549 (tm-30) cc_final: 0.7890 (tm-30) REVERT: G 53 GLN cc_start: 0.9250 (mm-40) cc_final: 0.9049 (mm110) REVERT: F 49 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8298 (tm-30) REVERT: F 80 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7609 (mm-30) outliers start: 57 outliers final: 24 residues processed: 210 average time/residue: 0.0817 time to fit residues: 24.4771 Evaluate side-chains 180 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 109 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 ASN C 38 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN E 108 GLN G 38 ASN F 14 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.055635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042248 restraints weight = 43809.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043566 restraints weight = 21258.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.044474 restraints weight = 13420.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.045070 restraints weight = 9798.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.045391 restraints weight = 7942.137| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10428 Z= 0.168 Angle : 0.637 7.162 14339 Z= 0.357 Chirality : 0.046 0.295 1632 Planarity : 0.004 0.040 1658 Dihedral : 21.492 164.377 1828 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.50 % Favored : 92.13 % Rotamer: Outliers : 4.07 % Allowed : 23.41 % Favored : 72.52 % 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: -0.31 (0.26), residues: 1080 helix: 0.12 (0.24), residues: 464 sheet: 1.10 (0.32), residues: 272 loop : -1.69 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 34 TYR 0.021 0.001 TYR F 51 PHE 0.019 0.001 PHE C 58 TRP 0.011 0.002 TRP D 115 HIS 0.004 0.002 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (10428) covalent geometry : angle 0.63666 / 0.36 (14339) hydrogen bonds : bond 0.04277 / 2.83 ( 517) hydrogen bonds : angle 5.14336 / 3.64 ( 1423) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.355 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: A 51 TYR cc_start: 0.9198 (t80) cc_final: 0.8979 (t80) REVERT: C 33 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7941 (p0) REVERT: C 49 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 53 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8334 (mm110) REVERT: C 62 GLN cc_start: 0.8889 (mt0) cc_final: 0.8684 (mm-40) REVERT: C 113 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6937 (mt-10) REVERT: B 49 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 61 THR cc_start: 0.9369 (p) cc_final: 0.9103 (p) REVERT: B 95 SER cc_start: 0.8929 (t) cc_final: 0.8665 (p) REVERT: B 122 GLN cc_start: 0.8823 (tp40) cc_final: 0.8436 (tp-100) REVERT: E 88 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7907 (pp) REVERT: D 98 LYS cc_start: 0.9180 (mtpp) cc_final: 0.8899 (mtmm) REVERT: G 49 GLU cc_start: 0.8573 (tm-30) cc_final: 0.7906 (tm-30) REVERT: G 53 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8869 (mm110) REVERT: F 49 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8277 (tm-30) REVERT: F 80 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7514 (mm-30) outliers start: 41 outliers final: 25 residues processed: 205 average time/residue: 0.0858 time to fit residues: 25.0300 Evaluate side-chains 180 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 109 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.055806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.042472 restraints weight = 43536.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.043817 restraints weight = 20895.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.044655 restraints weight = 13058.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.045290 restraints weight = 9712.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.045645 restraints weight = 7735.737| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10428 Z= 0.177 Angle : 0.633 7.192 14339 Z= 0.356 Chirality : 0.046 0.294 1632 Planarity : 0.004 0.068 1658 Dihedral : 21.466 165.183 1827 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.69 % Favored : 91.94 % Rotamer: Outliers : 4.07 % Allowed : 24.21 % Favored : 71.73 % 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: -0.32 (0.26), residues: 1080 helix: 0.14 (0.24), residues: 464 sheet: 1.02 (0.32), residues: 272 loop : -1.65 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 43 TYR 0.026 0.001 TYR F 51 PHE 0.023 0.001 PHE C 58 TRP 0.012 0.002 TRP D 115 HIS 0.004 0.002 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (10428) covalent geometry : angle 0.63309 / 0.36 (14339) hydrogen bonds : bond 0.04134 / 2.75 ( 517) hydrogen bonds : angle 5.00727 / 3.54 ( 1423) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.244 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: A 101 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8694 (mmmt) REVERT: C 49 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8491 (tm-30) REVERT: C 69 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8882 (mtmm) REVERT: C 113 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7042 (mt-10) REVERT: B 49 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7951 (tm-30) REVERT: B 62 GLN cc_start: 0.7896 (mp10) cc_final: 0.7688 (mp10) REVERT: B 122 GLN cc_start: 0.8932 (tp40) cc_final: 0.8493 (tp-100) REVERT: E 27 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7864 (p0) REVERT: E 88 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7894 (pp) REVERT: D 49 GLU cc_start: 0.8676 (tp30) cc_final: 0.8176 (tp30) REVERT: D 53 GLN cc_start: 0.9405 (mm-40) cc_final: 0.9010 (mm-40) REVERT: G 49 GLU cc_start: 0.8663 (tm-30) cc_final: 0.7921 (tm-30) REVERT: G 53 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8978 (mm110) REVERT: G 113 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7013 (mt-10) REVERT: G 117 LYS cc_start: 0.9347 (tptm) cc_final: 0.9076 (mmmm) REVERT: F 49 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8337 (tm-30) REVERT: F 80 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7448 (mm-30) outliers start: 41 outliers final: 29 residues processed: 195 average time/residue: 0.0810 time to fit residues: 22.5415 Evaluate side-chains 178 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 109 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0470 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** 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 = 0.3280 r_free = 0.3280 target = 0.054548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041454 restraints weight = 45780.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042745 restraints weight = 23456.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.043638 restraints weight = 15233.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044213 restraints weight = 11328.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.044619 restraints weight = 9284.529| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10428 Z= 0.203 Angle : 0.640 9.910 14339 Z= 0.356 Chirality : 0.046 0.292 1632 Planarity : 0.004 0.042 1658 Dihedral : 21.465 165.868 1827 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.22 % Favored : 92.31 % Rotamer: Outliers : 4.46 % Allowed : 23.12 % Favored : 72.42 % 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: -0.32 (0.26), residues: 1080 helix: 0.13 (0.24), residues: 464 sheet: 1.00 (0.32), residues: 272 loop : -1.60 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 43 TYR 0.014 0.002 TYR B 120 PHE 0.025 0.002 PHE C 48 TRP 0.011 0.002 TRP A 115 HIS 0.004 0.002 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (10428) covalent geometry : angle 0.63955 / 0.36 (14339) hydrogen bonds : bond 0.04205 / 2.73 ( 517) hydrogen bonds : angle 4.96449 / 3.51 ( 1423) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.377 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: C 49 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8481 (tm-30) REVERT: C 69 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8874 (mtmm) REVERT: C 113 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7137 (mt-10) REVERT: B 13 LYS cc_start: 0.9396 (mtpt) cc_final: 0.9113 (mtmm) REVERT: B 49 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B 122 GLN cc_start: 0.8933 (tp40) cc_final: 0.8445 (tp-100) REVERT: E 88 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7874 (pp) REVERT: D 49 GLU cc_start: 0.8655 (tp30) cc_final: 0.8067 (tp30) REVERT: D 53 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8990 (mm-40) REVERT: G 49 GLU cc_start: 0.8660 (tm-30) cc_final: 0.7893 (tm-30) REVERT: G 53 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8960 (mm110) REVERT: G 54 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9062 (p) REVERT: G 108 GLN cc_start: 0.7872 (mp10) cc_final: 0.7261 (mp10) REVERT: G 113 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6993 (mt-10) REVERT: G 117 LYS cc_start: 0.9382 (tptm) cc_final: 0.9096 (mmmm) REVERT: F 49 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8351 (tm-30) REVERT: F 80 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7413 (mm-30) REVERT: F 122 GLN cc_start: 0.8690 (mp10) cc_final: 0.8296 (mp10) outliers start: 45 outliers final: 35 residues processed: 190 average time/residue: 0.1001 time to fit residues: 27.2337 Evaluate side-chains 188 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 109 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** 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 = 0.3328 r_free = 0.3328 target = 0.056397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.042602 restraints weight = 44211.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.043954 restraints weight = 21794.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044920 restraints weight = 13901.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.045552 restraints weight = 10139.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.045899 restraints weight = 8189.746| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10428 Z= 0.158 Angle : 0.615 7.518 14339 Z= 0.342 Chirality : 0.046 0.293 1632 Planarity : 0.004 0.041 1658 Dihedral : 21.456 166.477 1827 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.50 % Favored : 92.04 % Rotamer: Outliers : 3.97 % Allowed : 24.31 % Favored : 71.73 % 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: -0.28 (0.26), residues: 1080 helix: 0.17 (0.24), residues: 464 sheet: 0.98 (0.32), residues: 272 loop : -1.57 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 43 TYR 0.009 0.001 TYR B 120 PHE 0.023 0.001 PHE C 58 TRP 0.011 0.002 TRP A 115 HIS 0.004 0.002 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (10428) covalent geometry : angle 0.61469 / 0.34 (14339) hydrogen bonds : bond 0.03773 / 2.48 ( 517) hydrogen bonds : angle 4.83890 / 3.43 ( 1423) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.407 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: C 49 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 53 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8407 (mm110) REVERT: C 69 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8846 (mtmm) REVERT: C 113 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7107 (mt-10) REVERT: B 13 LYS cc_start: 0.9393 (mtpt) cc_final: 0.9087 (mtmm) REVERT: B 26 PHE cc_start: 0.8622 (m-80) cc_final: 0.8408 (m-80) REVERT: B 49 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8071 (tm-30) REVERT: B 62 GLN cc_start: 0.8018 (mp10) cc_final: 0.7785 (mp10) REVERT: B 122 GLN cc_start: 0.8931 (tp40) cc_final: 0.8395 (tp-100) REVERT: E 88 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7851 (pp) REVERT: D 49 GLU cc_start: 0.8698 (tp30) cc_final: 0.8052 (tp30) REVERT: D 53 GLN cc_start: 0.9412 (mm-40) cc_final: 0.8969 (mm-40) REVERT: G 49 GLU cc_start: 0.8683 (tm-30) cc_final: 0.7917 (tm-30) REVERT: G 53 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8953 (mm110) REVERT: G 108 GLN cc_start: 0.7931 (mp10) cc_final: 0.7346 (mp10) REVERT: G 113 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6894 (mt-10) REVERT: G 117 LYS cc_start: 0.9397 (tptm) cc_final: 0.9082 (mmmm) REVERT: F 41 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7627 (mt-10) REVERT: F 49 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8378 (tm-30) REVERT: F 80 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7594 (mm-30) outliers start: 40 outliers final: 28 residues processed: 193 average time/residue: 0.1055 time to fit residues: 28.8531 Evaluate side-chains 179 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain F residue 55 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.053243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.040061 restraints weight = 46649.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.041336 restraints weight = 24418.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.042202 restraints weight = 16090.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.042777 restraints weight = 12153.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.043144 restraints weight = 10009.205| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 10428 Z= 0.298 Angle : 0.685 6.594 14339 Z= 0.373 Chirality : 0.047 0.283 1632 Planarity : 0.004 0.044 1658 Dihedral : 21.501 167.451 1825 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.87 % Favored : 91.67 % Rotamer: Outliers : 4.37 % Allowed : 24.90 % Favored : 70.73 % 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: -0.30 (0.26), residues: 1080 helix: 0.20 (0.24), residues: 456 sheet: 0.91 (0.32), residues: 272 loop : -1.55 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 43 TYR 0.014 0.002 TYR B 120 PHE 0.025 0.002 PHE A 52 TRP 0.014 0.002 TRP A 115 HIS 0.004 0.001 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.30 (10428) covalent geometry : angle 0.68459 / 0.37 (14339) hydrogen bonds : bond 0.04848 / 3.09 ( 517) hydrogen bonds : angle 5.04180 / 3.57 ( 1423) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.369 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: A 121 GLU cc_start: 0.8847 (tp30) cc_final: 0.8610 (tp30) REVERT: H 121 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8575 (mm-30) REVERT: C 49 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8466 (tm-30) REVERT: C 69 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8864 (mtmm) REVERT: C 113 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7046 (mt-10) REVERT: B 13 LYS cc_start: 0.9396 (mtpt) cc_final: 0.9071 (mtmm) REVERT: B 49 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8172 (tm-30) REVERT: B 95 SER cc_start: 0.8934 (t) cc_final: 0.8657 (p) REVERT: B 122 GLN cc_start: 0.8972 (tp40) cc_final: 0.8472 (tp-100) REVERT: E 88 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7851 (pp) REVERT: D 49 GLU cc_start: 0.8714 (tp30) cc_final: 0.8061 (tp30) REVERT: D 53 GLN cc_start: 0.9396 (mm-40) cc_final: 0.8910 (mm-40) REVERT: D 101 LYS cc_start: 0.9288 (mmmm) cc_final: 0.8863 (mmmm) REVERT: G 49 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8176 (tm-30) REVERT: G 53 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8966 (mm-40) REVERT: G 108 GLN cc_start: 0.8082 (mp10) cc_final: 0.7431 (mp10) REVERT: G 113 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7043 (mt-10) REVERT: G 117 LYS cc_start: 0.9436 (tptm) cc_final: 0.9108 (mmmm) REVERT: F 49 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8462 (tm-30) REVERT: F 80 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7549 (mm-30) REVERT: F 122 GLN cc_start: 0.8758 (mp10) cc_final: 0.8465 (mp10) outliers start: 44 outliers final: 31 residues processed: 180 average time/residue: 0.1009 time to fit residues: 25.8653 Evaluate side-chains 178 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain G residue 24 SER Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 103 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN A 119 GLN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.042583 restraints weight = 44040.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.043897 restraints weight = 21701.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.044812 restraints weight = 13759.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045408 restraints weight = 10072.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.045774 restraints weight = 8158.491| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10428 Z= 0.150 Angle : 0.625 7.417 14339 Z= 0.346 Chirality : 0.046 0.292 1632 Planarity : 0.004 0.042 1658 Dihedral : 21.467 167.759 1823 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.94 % Favored : 92.50 % Rotamer: Outliers : 3.27 % Allowed : 25.79 % Favored : 70.93 % 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: -0.26 (0.26), residues: 1080 helix: 0.23 (0.25), residues: 456 sheet: 0.97 (0.32), residues: 272 loop : -1.55 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 70 TYR 0.008 0.001 TYR A 123 PHE 0.021 0.001 PHE A 52 TRP 0.012 0.002 TRP A 115 HIS 0.004 0.002 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (10428) covalent geometry : angle 0.62524 / 0.35 (14339) hydrogen bonds : bond 0.03584 / 2.35 ( 517) hydrogen bonds : angle 4.83379 / 3.41 ( 1423) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8776 (tp30) cc_final: 0.8533 (tp30) REVERT: C 49 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8336 (tm-30) REVERT: C 53 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8408 (mm110) REVERT: C 69 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8849 (mtmm) REVERT: C 113 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7170 (mt-10) REVERT: B 13 LYS cc_start: 0.9359 (mtpt) cc_final: 0.9041 (mtmm) REVERT: B 49 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8082 (tm-30) REVERT: B 95 SER cc_start: 0.8837 (t) cc_final: 0.8566 (p) REVERT: B 122 GLN cc_start: 0.8866 (tp40) cc_final: 0.8324 (tp-100) REVERT: E 88 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7831 (pp) REVERT: D 49 GLU cc_start: 0.8690 (tp30) cc_final: 0.8025 (tp30) REVERT: D 53 GLN cc_start: 0.9365 (mm-40) cc_final: 0.8926 (mm-40) REVERT: D 101 LYS cc_start: 0.9274 (mmmm) cc_final: 0.8923 (mmmm) REVERT: G 49 GLU cc_start: 0.8705 (tm-30) cc_final: 0.7954 (tm-30) REVERT: G 53 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8940 (mm110) REVERT: G 108 GLN cc_start: 0.7947 (mp10) cc_final: 0.7386 (mp10) REVERT: G 113 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6889 (mt-10) REVERT: G 117 LYS cc_start: 0.9443 (tptm) cc_final: 0.9050 (mmmm) REVERT: F 41 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7607 (mt-10) REVERT: F 49 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8392 (tm-30) REVERT: F 55 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8616 (t80) REVERT: F 80 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7628 (mm-30) outliers start: 33 outliers final: 27 residues processed: 187 average time/residue: 0.1012 time to fit residues: 26.9194 Evaluate side-chains 177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain F residue 55 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN A 119 GLN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN G 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.054841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.041466 restraints weight = 44528.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.042753 restraints weight = 21946.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.043648 restraints weight = 13979.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044266 restraints weight = 10299.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044643 restraints weight = 8306.153| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10428 Z= 0.231 Angle : 0.652 7.008 14339 Z= 0.360 Chirality : 0.046 0.285 1632 Planarity : 0.004 0.044 1658 Dihedral : 21.488 168.678 1823 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.41 % Favored : 92.04 % Rotamer: Outliers : 3.67 % Allowed : 26.19 % Favored : 70.14 % 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: -0.29 (0.26), residues: 1080 helix: 0.18 (0.24), residues: 456 sheet: 0.94 (0.32), residues: 272 loop : -1.52 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 70 TYR 0.014 0.001 TYR A 120 PHE 0.041 0.002 PHE B 52 TRP 0.012 0.002 TRP B 115 HIS 0.005 0.002 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 (10428) covalent geometry : angle 0.65219 / 0.36 (14339) hydrogen bonds : bond 0.04135 / 2.65 ( 517) hydrogen bonds : angle 4.90586 / 3.47 ( 1423) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8866 (tp30) cc_final: 0.8621 (tp30) REVERT: H 27 ASP cc_start: 0.8220 (p0) cc_final: 0.7836 (p0) REVERT: C 27 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8556 (p0) REVERT: C 49 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8347 (tm-30) REVERT: C 53 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8443 (mm110) REVERT: C 69 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8825 (mtmm) REVERT: C 113 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7011 (mt-10) REVERT: B 13 LYS cc_start: 0.9382 (mtpt) cc_final: 0.9053 (mtmm) REVERT: B 49 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8134 (tm-30) REVERT: B 95 SER cc_start: 0.8841 (t) cc_final: 0.8557 (p) REVERT: B 122 GLN cc_start: 0.8910 (tp40) cc_final: 0.8376 (tp-100) REVERT: E 34 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7765 (tmt90) REVERT: D 49 GLU cc_start: 0.8727 (tp30) cc_final: 0.8044 (tp30) REVERT: D 53 GLN cc_start: 0.9396 (mm-40) cc_final: 0.8954 (mm-40) REVERT: D 101 LYS cc_start: 0.9289 (mmmm) cc_final: 0.8909 (mmmm) REVERT: G 49 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8230 (tm-30) REVERT: G 53 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8965 (mm-40) REVERT: G 108 GLN cc_start: 0.8020 (mp10) cc_final: 0.7385 (mp10) REVERT: G 113 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6910 (mt-10) REVERT: G 117 LYS cc_start: 0.9473 (tptm) cc_final: 0.9164 (mmmm) REVERT: G 119 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.8686 (mm-40) REVERT: F 41 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7681 (mt-10) REVERT: F 49 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8489 (tm-30) outliers start: 37 outliers final: 25 residues processed: 180 average time/residue: 0.0998 time to fit residues: 25.4666 Evaluate side-chains 176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 55 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN A 119 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.055890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.042384 restraints weight = 43620.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.043687 restraints weight = 21793.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.044594 restraints weight = 13940.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045210 restraints weight = 10251.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.045647 restraints weight = 8306.229| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10428 Z= 0.149 Angle : 0.642 8.007 14339 Z= 0.357 Chirality : 0.046 0.289 1632 Planarity : 0.004 0.043 1658 Dihedral : 21.477 168.877 1823 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.04 % Favored : 92.41 % Rotamer: Outliers : 2.88 % Allowed : 27.58 % Favored : 69.54 % 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: -0.33 (0.26), residues: 1080 helix: 0.13 (0.24), residues: 456 sheet: 0.94 (0.32), residues: 272 loop : -1.54 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 70 TYR 0.009 0.001 TYR B 120 PHE 0.038 0.002 PHE B 52 TRP 0.011 0.002 TRP A 115 HIS 0.005 0.002 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (10428) covalent geometry : angle 0.64223 / 0.36 (14339) hydrogen bonds : bond 0.03761 / 2.44 ( 517) hydrogen bonds : angle 4.84704 / 3.42 ( 1423) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8781 (tp30) cc_final: 0.8532 (tp30) REVERT: C 27 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8451 (p0) REVERT: C 49 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8301 (tm-30) REVERT: C 53 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8390 (mm110) REVERT: C 69 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8819 (mtmm) REVERT: C 113 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7217 (mt-10) REVERT: B 13 LYS cc_start: 0.9350 (mtpt) cc_final: 0.9026 (mtmm) REVERT: B 49 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8090 (tm-30) REVERT: B 95 SER cc_start: 0.8793 (t) cc_final: 0.8512 (p) REVERT: B 122 GLN cc_start: 0.8880 (tp40) cc_final: 0.8342 (tp-100) REVERT: E 34 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7757 (tmt90) REVERT: D 49 GLU cc_start: 0.8701 (tp30) cc_final: 0.8026 (tp30) REVERT: D 53 GLN cc_start: 0.9346 (mm-40) cc_final: 0.8908 (mm-40) REVERT: D 101 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8880 (mmmm) REVERT: G 49 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8002 (tm-30) REVERT: G 53 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8968 (mm110) REVERT: G 108 GLN cc_start: 0.7946 (mp10) cc_final: 0.7415 (mp10) REVERT: G 113 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6859 (mt-10) REVERT: G 117 LYS cc_start: 0.9440 (tptm) cc_final: 0.9175 (mmmm) REVERT: F 41 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7663 (mt-10) REVERT: F 49 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8445 (tm-30) REVERT: F 55 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8637 (t80) REVERT: F 80 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7542 (mm-30) outliers start: 29 outliers final: 22 residues processed: 181 average time/residue: 0.1008 time to fit residues: 26.0633 Evaluate side-chains 173 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 55 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN A 119 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.053493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.040012 restraints weight = 44545.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.041242 restraints weight = 22812.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.042093 restraints weight = 14900.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.042656 restraints weight = 11167.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.043067 restraints weight = 9177.193| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 10428 Z= 0.290 Angle : 0.702 6.953 14339 Z= 0.387 Chirality : 0.047 0.278 1632 Planarity : 0.004 0.044 1658 Dihedral : 21.518 169.850 1823 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.96 % Favored : 91.48 % Rotamer: Outliers : 3.27 % Allowed : 27.28 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.26), residues: 1080 helix: 0.04 (0.24), residues: 456 sheet: 0.83 (0.32), residues: 272 loop : -1.51 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 70 TYR 0.013 0.002 TYR B 120 PHE 0.032 0.002 PHE A 52 TRP 0.015 0.002 TRP B 115 HIS 0.004 0.002 HIS H 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.29 (10428) covalent geometry : angle 0.70175 / 0.39 (14339) hydrogen bonds : bond 0.04703 / 3.00 ( 517) hydrogen bonds : angle 5.04864 / 3.56 ( 1423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1558.98 seconds wall clock time: 27 minutes 48.50 seconds (1668.50 seconds total)