Starting phenix.real_space_refine on Wed Aug 5 21:06:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0z_50119/08_2026/9f0z_50119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0z_50119/08_2026/9f0z_50119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f0z_50119/08_2026/9f0z_50119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0z_50119/08_2026/9f0z_50119.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0z_50119/08_2026/9f0z_50119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0z_50119/08_2026/9f0z_50119.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 181 5.49 5 Mg 1 5.21 5 S 30 5.16 5 C 6919 2.51 5 N 2190 2.21 5 O 2649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11970 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1982 Classifications: {'DNA': 96} Link IDs: {'rna3p': 95} Chain: "B" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1739 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 749 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "F" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 976 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 874 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 885 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4000 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 21, 'TRANS': 523} Chain breaks: 14 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TRP:plan': 1, 'GLN:plan1': 6, 'ARG:plan': 4, 'GLU:plan': 9, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.63, per 1000 atoms: 0.22 Number of scatterers: 11970 At special positions: 0 Unit cell: (95.7, 129.525, 181.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 181 15.00 Mg 1 11.99 O 2649 8.00 N 2190 7.00 C 6919 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: 0.82 Conformation dependent library (CDL) restraints added in 394.9 milliseconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 44.6% alpha, 16.2% beta 75 base pairs and 154 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.623A pdb=" N ILE C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 18 through 39 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'F' and resid 20 through 34 removed outlier: 4.135A pdb=" N SER F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 52 removed outlier: 3.662A pdb=" N ASP F 47 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 90 Processing helix chain 'F' and resid 92 through 108 Processing helix chain 'G' and resid 20 through 34 removed outlier: 4.030A pdb=" N SER G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 52 Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.848A pdb=" N LYS G 64 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 92 through 106 removed outlier: 4.546A pdb=" N ARG G 100 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 34 removed outlier: 4.165A pdb=" N SER E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU E 25 " --> pdb=" O ASP E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 52 Processing helix chain 'E' and resid 75 through 90 Processing helix chain 'E' and resid 92 through 108 Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.862A pdb=" N ASN H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 42 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 87 through 95 removed outlier: 4.072A pdb=" N SER H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 111 removed outlier: 4.026A pdb=" N ALA H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 192 Processing helix chain 'H' and resid 192 through 212 removed outlier: 3.697A pdb=" N GLU H 202 " --> pdb=" O ARG H 198 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU H 204 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA H 210 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 222 removed outlier: 3.592A pdb=" N GLY H 222 " --> pdb=" O GLY H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 219 through 222' Processing helix chain 'H' and resid 228 through 232 Processing helix chain 'H' and resid 235 through 246 Processing helix chain 'H' and resid 251 through 252 No H-bonds generated for 'chain 'H' and resid 251 through 252' Processing helix chain 'H' and resid 254 through 254 No H-bonds generated for 'chain 'H' and resid 254 through 254' Processing helix chain 'H' and resid 255 through 262 Processing helix chain 'H' and resid 269 through 281 Processing helix chain 'H' and resid 291 through 296 removed outlier: 3.901A pdb=" N ASP H 296 " --> pdb=" O ARG H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 575 through 593 Processing helix chain 'H' and resid 603 through 622 Processing helix chain 'H' and resid 646 through 650 removed outlier: 3.755A pdb=" N MET H 649 " --> pdb=" O LEU H 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 696 through 698 No H-bonds generated for 'chain 'H' and resid 696 through 698' Processing helix chain 'H' and resid 763 through 767 Processing helix chain 'H' and resid 798 through 808 Processing helix chain 'H' and resid 822 through 828 removed outlier: 4.025A pdb=" N ALA H 828 " --> pdb=" O GLU H 825 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46 removed outlier: 3.646A pdb=" N VAL C 44 " --> pdb=" O PHE C 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 45 Processing sheet with id=AA3, first strand: chain 'F' and resid 13 through 19 Processing sheet with id=AA4, first strand: chain 'G' and resid 13 through 19 Processing sheet with id=AA5, first strand: chain 'E' and resid 13 through 19 Processing sheet with id=AA6, first strand: chain 'H' and resid 4 through 6 removed outlier: 5.060A pdb=" N GLN H 155 " --> pdb=" O THR H 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AA8, first strand: chain 'H' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AB1, first strand: chain 'H' and resid 568 through 572 removed outlier: 6.267A pdb=" N THR H 569 " --> pdb=" O LEU H 814 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER H 816 " --> pdb=" O THR H 569 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE H 571 " --> pdb=" O SER H 816 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA H 790 " --> pdb=" O ARG H 813 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL H 598 " --> pdb=" O PHE H 789 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER H 791 " --> pdb=" O VAL H 598 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN H 600 " --> pdb=" O SER H 791 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLU H 776 " --> pdb=" O SER H 597 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA H 599 " --> pdb=" O GLU H 776 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 629 through 636 removed outlier: 3.528A pdb=" N SER H 665 " --> pdb=" O ASN H 660 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR H 682 " --> pdb=" O ASP H 672 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL H 674 " --> pdb=" O SER H 680 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER H 680 " --> pdb=" O VAL H 674 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 756 through 759 removed outlier: 4.190A pdb=" N SER H 739 " --> pdb=" O THR H 746 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL H 748 " --> pdb=" O VAL H 737 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL H 737 " --> pdb=" O VAL H 748 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 169 hydrogen bonds 334 hydrogen bond angles 0 basepair planarities 75 basepair parallelities 154 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.16 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: 2705 1.33 - 1.45: 3299 1.45 - 1.57: 6125 1.57 - 1.69: 360 1.69 - 1.81: 57 Bond restraints: 12546 Sorted by residual: bond pdb=" C3' DT A 88 " pdb=" C2' DT A 88 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.48e+01 bond pdb=" C3' DC B 75 " pdb=" C2' DC B 75 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DG A 17 " pdb=" C2' DG A 17 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DG B 10 " pdb=" C2' DG B 10 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG B 85 " pdb=" C2' DG B 85 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 ... (remaining 12541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 15930 1.07 - 2.15: 1273 2.15 - 3.22: 475 3.22 - 4.29: 28 4.29 - 5.36: 7 Bond angle restraints: 17713 Sorted by residual: angle pdb=" O4' DA A 41 " pdb=" C4' DA A 41 " pdb=" C3' DA A 41 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.37e+01 angle pdb=" O4' DT A 46 " pdb=" C4' DT A 46 " pdb=" C3' DT A 46 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N3 DT B 35 " pdb=" C4 DT B 35 " pdb=" O4 DT B 35 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" O4' DG A 5 " pdb=" C4' DG A 5 " pdb=" C3' DG A 5 " ideal model delta sigma weight residual 106.00 103.35 2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" O4' DC B 27 " pdb=" C4' DC B 27 " pdb=" C3' DC B 27 " ideal model delta sigma weight residual 106.00 103.39 2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 17708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.33: 6331 34.33 - 68.66: 834 68.66 - 103.00: 13 103.00 - 137.33: 1 137.33 - 171.66: 1 Dihedral angle restraints: 7180 sinusoidal: 4109 harmonic: 3071 Sorted by residual: dihedral pdb=" CA PHE G 108 " pdb=" C PHE G 108 " pdb=" N PRO G 109 " pdb=" CA PRO G 109 " ideal model delta harmonic sigma weight residual 180.00 156.71 23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU H 26 " pdb=" C LEU H 26 " pdb=" N GLY H 27 " pdb=" CA GLY H 27 " ideal model delta harmonic sigma weight residual -180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C4' DG A 5 " pdb=" C3' DG A 5 " pdb=" O3' DG A 5 " pdb=" P DG A 4 " ideal model delta sinusoidal sigma weight residual 220.00 48.34 171.66 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1227 0.031 - 0.062: 472 0.062 - 0.093: 196 0.093 - 0.125: 74 0.125 - 0.156: 13 Chirality restraints: 1982 Sorted by residual: chirality pdb=" C3' DA A 50 " pdb=" C4' DA A 50 " pdb=" O3' DA A 50 " pdb=" C2' DA A 50 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" C3' DA B 44 " pdb=" C4' DA B 44 " pdb=" O3' DA B 44 " pdb=" C2' DA B 44 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" C1' DG A -1 " pdb=" O4' DG A -1 " pdb=" C2' DG A -1 " pdb=" N9 DG A -1 " both_signs ideal model delta sigma weight residual False 2.43 2.29 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1979 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA A 21 " 0.028 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA A 21 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA A 21 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA A 21 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA A 21 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA A 21 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA A 21 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA A 21 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA A 21 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA A 21 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA A 21 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA A 41 " -0.026 2.00e-02 2.50e+03 1.17e-02 3.75e+00 pdb=" N9 DA A 41 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA A 41 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA A 41 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA A 41 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA A 41 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA A 41 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA A 41 " -0.006 2.00e-02 2.50e+03 pdb=" C2 DA A 41 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DA A 41 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA A 41 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 60 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO H 61 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " -0.025 5.00e-02 4.00e+02 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 76 2.53 - 3.12: 8600 3.12 - 3.72: 20244 3.72 - 4.31: 27580 4.31 - 4.90: 42299 Nonbonded interactions: 98799 Sorted by model distance: nonbonded pdb=" OP1 DG A -1 " pdb="MG MG H 900 " model vdw 1.940 2.170 nonbonded pdb=" ND1 HIS H 146 " pdb="MG MG H 900 " model vdw 2.020 2.250 nonbonded pdb=" NE2 HIS H 159 " pdb="MG MG H 900 " model vdw 2.046 2.250 nonbonded pdb=" NE2 HIS H 157 " pdb="MG MG H 900 " model vdw 2.110 2.250 nonbonded pdb=" OG SER G 89 " pdb=" OE2 GLU G 96 " model vdw 2.133 3.040 ... (remaining 98794 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 'E' and (resid 11 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 or (resid 56 and (name N or name CA or nam \ e C or name O or name CB )) or resid 57 through 75 or (resid 76 through 77 and ( \ name N or name CA or name C or name O or name CB )) or resid 78 through 113)) selection = (chain 'F' and (resid 11 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 or (resid 56 and (name N or name CA or nam \ e C or name O or name CB )) or resid 57 through 59 or resid 63 or (resid 64 and \ (name N or name CA or name C or name O or name CB )) or resid 65 through 75 or ( \ resid 76 through 77 and (name N or name CA or name C or name O or name CB )) or \ resid 78 through 113)) selection = (chain 'G' and (resid 11 through 59 or resid 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 113)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.320 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.710 Find NCS groups from input model: 0.100 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 0.038 12546 Z= 0.458 Angle : 0.695 5.364 17713 Z= 0.619 Chirality : 0.042 0.156 1982 Planarity : 0.004 0.044 1654 Dihedral : 22.917 171.661 5186 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.82 % Allowed : 3.87 % Favored : 95.31 % 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: 0.22 (0.26), residues: 1031 helix: 1.06 (0.24), residues: 439 sheet: -0.03 (0.38), residues: 201 loop : -0.71 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 32 TYR 0.013 0.001 TYR G 112 PHE 0.011 0.001 PHE E 4 TRP 0.004 0.001 TRP H 702 HIS 0.006 0.001 HIS H 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.46 (12546) covalent geometry : angle 0.69505 / 0.62 (17713) hydrogen bonds : bond 0.13029 / 14.21 ( 573) hydrogen bonds : angle 6.03602 / 8.25 ( 1474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 241 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 THR cc_start: 0.6857 (p) cc_final: 0.6556 (p) REVERT: F 95 ASP cc_start: 0.8513 (m-30) cc_final: 0.8243 (m-30) REVERT: G 111 PHE cc_start: 0.6359 (t80) cc_final: 0.6087 (t80) REVERT: H 17 TYR cc_start: 0.7901 (m-80) cc_final: 0.7682 (m-80) REVERT: H 223 MET cc_start: 0.5359 (mmm) cc_final: 0.4534 (mmm) REVERT: H 267 HIS cc_start: 0.5878 (t70) cc_final: 0.5430 (t-90) REVERT: H 621 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7850 (mm110) REVERT: H 815 TYR cc_start: 0.7933 (m-80) cc_final: 0.7434 (m-80) outliers start: 7 outliers final: 1 residues processed: 248 average time/residue: 0.1276 time to fit residues: 43.0362 Evaluate side-chains 118 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 138 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS H 106 HIS H 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.081419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.064808 restraints weight = 56368.283| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.73 r_work: 0.3283 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12546 Z= 0.279 Angle : 0.800 14.709 17713 Z= 0.443 Chirality : 0.049 0.363 1982 Planarity : 0.006 0.055 1654 Dihedral : 27.726 169.663 3240 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.70 % Allowed : 11.97 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.20 (0.25), residues: 1031 helix: 0.75 (0.24), residues: 437 sheet: -0.29 (0.35), residues: 207 loop : -0.96 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 88 TYR 0.020 0.002 TYR H 213 PHE 0.028 0.003 PHE D 51 TRP 0.012 0.002 TRP H 638 HIS 0.015 0.002 HIS F 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.28 (12546) covalent geometry : angle 0.79992 / 0.44 (17713) hydrogen bonds : bond 0.06004 / 6.51 ( 573) hydrogen bonds : angle 5.11015 / 6.96 ( 1474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 THR cc_start: 0.6988 (p) cc_final: 0.6773 (p) REVERT: F 40 GLU cc_start: 0.8419 (tp30) cc_final: 0.7979 (tp30) REVERT: F 80 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8166 (mm-40) REVERT: F 116 ILE cc_start: 0.8510 (mm) cc_final: 0.8103 (mm) REVERT: G 93 LYS cc_start: 0.4932 (tttt) cc_final: 0.3648 (mttt) REVERT: G 111 PHE cc_start: 0.6565 (t80) cc_final: 0.6341 (t80) REVERT: H 2 MET cc_start: 0.6404 (mtp) cc_final: 0.6054 (mtp) REVERT: H 147 ASP cc_start: 0.7203 (p0) cc_final: 0.6983 (p0) REVERT: H 223 MET cc_start: 0.4549 (mmm) cc_final: 0.4269 (mmm) REVERT: H 267 HIS cc_start: 0.5876 (t70) cc_final: 0.5400 (t-90) outliers start: 23 outliers final: 11 residues processed: 138 average time/residue: 0.0884 time to fit residues: 18.7184 Evaluate side-chains 111 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 700 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 107 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.0000 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 HIS ** 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 = 0.3972 r_free = 0.3972 target = 0.082521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.063979 restraints weight = 56042.665| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.80 r_work: 0.3333 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12546 Z= 0.157 Angle : 0.667 13.707 17713 Z= 0.382 Chirality : 0.044 0.332 1982 Planarity : 0.004 0.051 1654 Dihedral : 27.670 169.752 3238 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.64 % Allowed : 13.38 % Favored : 84.98 % 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: -0.01 (0.26), residues: 1031 helix: 0.92 (0.24), residues: 433 sheet: -0.26 (0.36), residues: 206 loop : -0.81 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 57 TYR 0.015 0.001 TYR H 815 PHE 0.022 0.002 PHE F 111 TRP 0.010 0.001 TRP H 277 HIS 0.009 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (12546) covalent geometry : angle 0.66671 / 0.38 (17713) hydrogen bonds : bond 0.04385 / 4.67 ( 573) hydrogen bonds : angle 4.79739 / 6.55 ( 1474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 THR cc_start: 0.6936 (p) cc_final: 0.6721 (p) REVERT: F 23 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8546 (tm-30) REVERT: F 40 GLU cc_start: 0.8296 (tp30) cc_final: 0.8014 (tp30) REVERT: F 80 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8147 (mm-40) REVERT: F 111 PHE cc_start: 0.6240 (t80) cc_final: 0.5788 (t80) REVERT: F 116 ILE cc_start: 0.8426 (mm) cc_final: 0.8126 (mm) REVERT: G 93 LYS cc_start: 0.4795 (tttt) cc_final: 0.3354 (mttm) REVERT: G 111 PHE cc_start: 0.6394 (t80) cc_final: 0.6149 (t80) REVERT: H 566 ARG cc_start: 0.5855 (OUTLIER) cc_final: 0.4868 (mtm-85) outliers start: 14 outliers final: 5 residues processed: 121 average time/residue: 0.0906 time to fit residues: 16.5526 Evaluate side-chains 105 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 801 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 121 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.081988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.063445 restraints weight = 56711.886| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.77 r_work: 0.3320 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12546 Z= 0.173 Angle : 0.668 12.782 17713 Z= 0.379 Chirality : 0.043 0.328 1982 Planarity : 0.004 0.049 1654 Dihedral : 27.717 167.437 3238 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.58 % Allowed : 13.03 % Favored : 84.39 % 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: -0.13 (0.26), residues: 1031 helix: 0.76 (0.24), residues: 445 sheet: -0.39 (0.36), residues: 206 loop : -0.79 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 57 TYR 0.009 0.001 TYR H 200 PHE 0.015 0.002 PHE F 111 TRP 0.005 0.001 TRP H 172 HIS 0.006 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (12546) covalent geometry : angle 0.66763 / 0.38 (17713) hydrogen bonds : bond 0.04511 / 4.83 ( 573) hydrogen bonds : angle 4.68237 / 6.39 ( 1474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 THR cc_start: 0.6999 (p) cc_final: 0.6791 (p) REVERT: F 23 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8638 (tm-30) REVERT: F 40 GLU cc_start: 0.8336 (tp30) cc_final: 0.8115 (tp30) REVERT: F 80 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8114 (mm-40) REVERT: G 93 LYS cc_start: 0.4894 (tttt) cc_final: 0.3406 (mttm) REVERT: G 111 PHE cc_start: 0.6459 (t80) cc_final: 0.6210 (t80) REVERT: H 566 ARG cc_start: 0.5940 (OUTLIER) cc_final: 0.4976 (mtm-85) REVERT: H 810 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7229 (ptt180) outliers start: 22 outliers final: 11 residues processed: 121 average time/residue: 0.0918 time to fit residues: 16.5386 Evaluate side-chains 110 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 0.0070 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 HIS ** 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 = 0.3955 r_free = 0.3955 target = 0.081700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.065071 restraints weight = 56800.858| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.79 r_work: 0.3299 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12546 Z= 0.179 Angle : 0.667 12.082 17713 Z= 0.378 Chirality : 0.043 0.315 1982 Planarity : 0.004 0.049 1654 Dihedral : 27.760 166.114 3238 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.82 % Allowed : 13.62 % Favored : 83.57 % 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: -0.13 (0.26), residues: 1031 helix: 0.84 (0.24), residues: 442 sheet: -0.60 (0.34), residues: 217 loop : -0.73 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 118 TYR 0.014 0.001 TYR H 200 PHE 0.031 0.002 PHE F 111 TRP 0.005 0.001 TRP H 702 HIS 0.005 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (12546) covalent geometry : angle 0.66744 / 0.38 (17713) hydrogen bonds : bond 0.04425 / 4.70 ( 573) hydrogen bonds : angle 4.63738 / 6.32 ( 1474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8620 (tm-30) REVERT: F 80 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8078 (mm-40) REVERT: F 111 PHE cc_start: 0.6200 (t80) cc_final: 0.5672 (t80) REVERT: G 93 LYS cc_start: 0.5045 (tttt) cc_final: 0.3409 (mttm) REVERT: G 111 PHE cc_start: 0.6572 (t80) cc_final: 0.6229 (t80) REVERT: H 566 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.4757 (mtm-85) REVERT: H 810 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7070 (ptt180) outliers start: 24 outliers final: 14 residues processed: 121 average time/residue: 0.0906 time to fit residues: 16.2354 Evaluate side-chains 111 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 0.0000 chunk 38 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 HIS ** 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 = 0.3960 r_free = 0.3960 target = 0.081831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.065273 restraints weight = 57309.332| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.78 r_work: 0.3301 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12546 Z= 0.165 Angle : 0.658 11.544 17713 Z= 0.371 Chirality : 0.042 0.299 1982 Planarity : 0.004 0.050 1654 Dihedral : 27.756 166.093 3238 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.05 % Allowed : 13.85 % Favored : 83.10 % 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: -0.11 (0.26), residues: 1031 helix: 0.85 (0.24), residues: 445 sheet: -0.59 (0.34), residues: 217 loop : -0.75 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 57 TYR 0.012 0.001 TYR H 200 PHE 0.025 0.002 PHE F 111 TRP 0.005 0.001 TRP H 702 HIS 0.004 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (12546) covalent geometry : angle 0.65838 / 0.37 (17713) hydrogen bonds : bond 0.04263 / 4.51 ( 573) hydrogen bonds : angle 4.59685 / 6.25 ( 1474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8588 (tm-30) REVERT: F 40 GLU cc_start: 0.8358 (tp30) cc_final: 0.7939 (tp30) REVERT: F 80 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8104 (mm-40) REVERT: F 111 PHE cc_start: 0.6290 (t80) cc_final: 0.5999 (t80) REVERT: G 93 LYS cc_start: 0.5033 (tttt) cc_final: 0.3714 (mttm) REVERT: G 111 PHE cc_start: 0.6607 (t80) cc_final: 0.6318 (t80) REVERT: H 2 MET cc_start: 0.6538 (mmm) cc_final: 0.6217 (mmm) REVERT: H 223 MET cc_start: 0.3600 (mmm) cc_final: 0.3066 (mmm) REVERT: H 566 ARG cc_start: 0.6009 (OUTLIER) cc_final: 0.4873 (mtm-85) REVERT: H 810 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7081 (ptt180) outliers start: 26 outliers final: 18 residues processed: 120 average time/residue: 0.0990 time to fit residues: 17.9536 Evaluate side-chains 116 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.0670 chunk 94 optimal weight: 0.4980 chunk 74 optimal weight: 0.0670 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 HIS ** 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 = 0.3973 r_free = 0.3973 target = 0.082315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.065780 restraints weight = 56719.958| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.82 r_work: 0.3317 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12546 Z= 0.144 Angle : 0.638 12.299 17713 Z= 0.359 Chirality : 0.041 0.288 1982 Planarity : 0.004 0.048 1654 Dihedral : 27.664 165.128 3238 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.35 % Allowed : 15.26 % Favored : 82.39 % 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: -0.02 (0.26), residues: 1031 helix: 0.94 (0.24), residues: 448 sheet: -0.54 (0.34), residues: 217 loop : -0.73 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 642 TYR 0.014 0.001 TYR H 200 PHE 0.021 0.002 PHE F 111 TRP 0.006 0.001 TRP H 277 HIS 0.004 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (12546) covalent geometry : angle 0.63764 / 0.36 (17713) hydrogen bonds : bond 0.03874 / 4.06 ( 573) hydrogen bonds : angle 4.43169 / 5.96 ( 1474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8578 (tm-30) REVERT: F 40 GLU cc_start: 0.8357 (tp30) cc_final: 0.7954 (tp30) REVERT: F 80 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8124 (mm-40) REVERT: F 111 PHE cc_start: 0.6202 (t80) cc_final: 0.5864 (t80) REVERT: G 37 ARG cc_start: 0.7959 (mmt180) cc_final: 0.7520 (mmt-90) REVERT: G 81 LEU cc_start: 0.3609 (OUTLIER) cc_final: 0.3344 (mm) REVERT: G 93 LYS cc_start: 0.4925 (tttt) cc_final: 0.3384 (mttm) REVERT: G 111 PHE cc_start: 0.6637 (t80) cc_final: 0.6235 (t80) REVERT: H 223 MET cc_start: 0.3550 (mmm) cc_final: 0.3039 (mmm) REVERT: H 810 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6898 (ptt180) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.0842 time to fit residues: 15.6736 Evaluate side-chains 113 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 663 THR Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 58 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.082506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.064151 restraints weight = 56595.323| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.80 r_work: 0.3343 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12546 Z= 0.139 Angle : 0.630 12.037 17713 Z= 0.356 Chirality : 0.040 0.277 1982 Planarity : 0.004 0.048 1654 Dihedral : 27.594 164.066 3238 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.70 % Allowed : 15.02 % Favored : 82.28 % 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: 0.13 (0.27), residues: 1031 helix: 1.10 (0.24), residues: 444 sheet: -0.57 (0.33), residues: 226 loop : -0.60 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 32 TYR 0.011 0.001 TYR H 200 PHE 0.020 0.002 PHE F 111 TRP 0.006 0.001 TRP H 277 HIS 0.005 0.001 HIS F 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (12546) covalent geometry : angle 0.63002 / 0.36 (17713) hydrogen bonds : bond 0.03852 / 4.03 ( 573) hydrogen bonds : angle 4.35847 / 5.88 ( 1474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8530 (tm-30) REVERT: F 40 GLU cc_start: 0.8327 (tp30) cc_final: 0.7926 (tp30) REVERT: F 80 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8117 (mm-40) REVERT: G 37 ARG cc_start: 0.8042 (mmt180) cc_final: 0.7628 (mmt-90) REVERT: G 93 LYS cc_start: 0.4932 (tttt) cc_final: 0.3393 (mttm) REVERT: G 111 PHE cc_start: 0.6568 (t80) cc_final: 0.6169 (t80) REVERT: H 144 PHE cc_start: 0.7015 (m-80) cc_final: 0.6789 (m-80) REVERT: H 223 MET cc_start: 0.3514 (mmm) cc_final: 0.2975 (mmm) REVERT: H 566 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.4852 (mtm-85) REVERT: H 810 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6902 (ptt180) outliers start: 23 outliers final: 18 residues processed: 119 average time/residue: 0.0908 time to fit residues: 16.4155 Evaluate side-chains 118 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 663 THR Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS H 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.082226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.063904 restraints weight = 56306.883| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.78 r_work: 0.3339 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12546 Z= 0.150 Angle : 0.643 13.284 17713 Z= 0.361 Chirality : 0.041 0.273 1982 Planarity : 0.004 0.058 1654 Dihedral : 27.595 163.116 3238 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.05 % Allowed : 15.02 % Favored : 81.92 % 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: 0.12 (0.27), residues: 1031 helix: 1.13 (0.25), residues: 442 sheet: -0.65 (0.33), residues: 227 loop : -0.60 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 118 TYR 0.011 0.001 TYR H 200 PHE 0.032 0.002 PHE F 111 TRP 0.007 0.001 TRP H 277 HIS 0.005 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (12546) covalent geometry : angle 0.64315 / 0.36 (17713) hydrogen bonds : bond 0.04004 / 4.20 ( 573) hydrogen bonds : angle 4.40774 / 5.99 ( 1474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8565 (tm-30) REVERT: F 40 GLU cc_start: 0.8336 (tp30) cc_final: 0.7945 (tp30) REVERT: G 37 ARG cc_start: 0.8018 (mmt180) cc_final: 0.7574 (mmt-90) REVERT: G 81 LEU cc_start: 0.3598 (OUTLIER) cc_final: 0.3329 (mm) REVERT: G 93 LYS cc_start: 0.4899 (tttt) cc_final: 0.3389 (mttm) REVERT: G 111 PHE cc_start: 0.6614 (t80) cc_final: 0.6184 (t80) REVERT: H 223 MET cc_start: 0.3532 (mmm) cc_final: 0.2991 (mmm) REVERT: H 566 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.4876 (mtm-85) REVERT: H 623 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.7223 (m) outliers start: 26 outliers final: 20 residues processed: 123 average time/residue: 0.0896 time to fit residues: 17.0118 Evaluate side-chains 116 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 623 VAL Chi-restraints excluded: chain H residue 663 THR Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 700 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 0.3980 chunk 91 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN H 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.082056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.065560 restraints weight = 56955.503| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.86 r_work: 0.3310 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12546 Z= 0.161 Angle : 0.655 13.807 17713 Z= 0.367 Chirality : 0.041 0.266 1982 Planarity : 0.004 0.055 1654 Dihedral : 27.618 162.286 3238 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.82 % Allowed : 16.08 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.27), residues: 1031 helix: 0.98 (0.24), residues: 448 sheet: -0.83 (0.32), residues: 234 loop : -0.60 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 752 TYR 0.010 0.001 TYR H 200 PHE 0.030 0.002 PHE F 111 TRP 0.005 0.001 TRP H 172 HIS 0.007 0.001 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (12546) covalent geometry : angle 0.65505 / 0.37 (17713) hydrogen bonds : bond 0.04120 / 4.34 ( 573) hydrogen bonds : angle 4.43133 / 5.99 ( 1474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8545 (tm-30) REVERT: F 40 GLU cc_start: 0.8389 (tp30) cc_final: 0.8015 (tp30) REVERT: F 111 PHE cc_start: 0.5782 (t80) cc_final: 0.5564 (t80) REVERT: G 37 ARG cc_start: 0.8089 (mmt180) cc_final: 0.7650 (mmt-90) REVERT: G 81 LEU cc_start: 0.3601 (OUTLIER) cc_final: 0.3344 (mm) REVERT: G 93 LYS cc_start: 0.4959 (tttt) cc_final: 0.3426 (mttm) REVERT: G 111 PHE cc_start: 0.6635 (t80) cc_final: 0.6128 (t80) REVERT: H 223 MET cc_start: 0.3617 (mmm) cc_final: 0.3094 (mmm) REVERT: H 566 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.4890 (mtm-85) REVERT: H 623 VAL cc_start: 0.7503 (OUTLIER) cc_final: 0.7145 (m) outliers start: 24 outliers final: 19 residues processed: 120 average time/residue: 0.0905 time to fit residues: 16.8251 Evaluate side-chains 116 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 566 ARG Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 623 VAL Chi-restraints excluded: chain H residue 663 THR Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 700 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.082353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.064070 restraints weight = 56427.365| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.78 r_work: 0.3343 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12546 Z= 0.145 Angle : 0.659 14.907 17713 Z= 0.366 Chirality : 0.041 0.322 1982 Planarity : 0.004 0.053 1654 Dihedral : 27.583 162.019 3238 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.46 % Allowed : 16.43 % Favored : 81.10 % 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: -0.07 (0.27), residues: 1031 helix: 0.94 (0.24), residues: 448 sheet: -0.81 (0.33), residues: 233 loop : -0.62 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 37 TYR 0.010 0.001 TYR H 200 PHE 0.027 0.001 PHE F 111 TRP 0.006 0.001 TRP H 277 HIS 0.005 0.001 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (12546) covalent geometry : angle 0.65863 / 0.37 (17713) hydrogen bonds : bond 0.03979 / 4.16 ( 573) hydrogen bonds : angle 4.39487 / 5.95 ( 1474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3140.15 seconds wall clock time: 54 minutes 21.70 seconds (3261.70 seconds total)