Starting phenix.real_space_refine on Fri Jul 3 03:09:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0z_50119/07_2026/9f0z_50119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0z_50119/07_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_50119/07_2026/9f0z_50119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0z_50119/07_2026/9f0z_50119.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0z_50119/07_2026/9f0z_50119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0z_50119/07_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-dev-6108/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: 2.26, per 1000 atoms: 0.19 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: 0.78 Conformation dependent library (CDL) restraints added in 405.2 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: 1.34 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: 2.77 Time building geometry restraints manager: 1.09 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: 15971 1.07 - 2.15: 1235 2.15 - 3.22: 472 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: 16.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.280 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.200 ------------------------------------------------------------------------------- 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 : 0.690 5.364 17713 Z= 0.615 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 0.69020 / 0.62 (17713) hydrogen bonds : bond 0.13029 / 14.12 ( 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 : 0.304 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: 0.8242 (m-30) REVERT: G 93 LYS cc_start: 0.5574 (tttt) cc_final: 0.4296 (mttt) 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: 0.1230 time to fit residues: 41.1163 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 : 0.289 ------------------------------------------------------------------------------- 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: 1.9990 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: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.081097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.064563 restraints weight = 56551.444| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.90 r_work: 0.3268 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 12546 Z= 0.314 Angle : 0.816 14.491 17713 Z= 0.453 Chirality : 0.050 0.335 1982 Planarity : 0.006 0.049 1654 Dihedral : 27.792 170.015 3240 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.58 % Allowed : 12.56 % Favored : 84.86 % 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 (0.25), residues: 1031 helix: 0.67 (0.23), residues: 437 sheet: -0.31 (0.35), residues: 207 loop : -1.00 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 88 TYR 0.018 0.003 TYR H 213 PHE 0.031 0.003 PHE D 51 TRP 0.011 0.002 TRP H 638 HIS 0.016 0.003 HIS F 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.31 (12546) covalent geometry : angle 0.81597 / 0.45 (17713) hydrogen bonds : bond 0.06346 / 6.87 ( 573) hydrogen bonds : angle 5.18421 / 7.06 ( 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 138 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 THR cc_start: 0.7021 (p) cc_final: 0.6814 (p) REVERT: F 40 GLU cc_start: 0.8455 (tp30) cc_final: 0.8018 (tp30) REVERT: F 80 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8183 (mm-40) REVERT: F 108 PHE cc_start: 0.8244 (m-10) cc_final: 0.8019 (m-80) REVERT: G 93 LYS cc_start: 0.5335 (tttt) cc_final: 0.4114 (mttt) REVERT: G 111 PHE cc_start: 0.6565 (t80) cc_final: 0.6356 (t80) REVERT: E 40 GLU cc_start: 0.8145 (tp30) cc_final: 0.7793 (tp30) REVERT: H 147 ASP cc_start: 0.7236 (p0) cc_final: 0.7027 (p0) REVERT: H 223 MET cc_start: 0.4508 (mmm) cc_final: 0.4176 (mmm) REVERT: H 267 HIS cc_start: 0.5820 (t70) cc_final: 0.5360 (t-90) outliers start: 22 outliers final: 11 residues processed: 134 average time/residue: 0.0902 time to fit residues: 18.4236 Evaluate side-chains 114 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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: 0.4980 chunk 7 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.081807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.065077 restraints weight = 56098.257| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.83 r_work: 0.3291 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12546 Z= 0.181 Angle : 0.677 13.744 17713 Z= 0.388 Chirality : 0.044 0.316 1982 Planarity : 0.005 0.049 1654 Dihedral : 27.797 170.219 3238 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.88 % Allowed : 14.20 % Favored : 83.92 % 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: -0.22 (0.26), residues: 1031 helix: 0.79 (0.24), residues: 438 sheet: -0.48 (0.36), residues: 212 loop : -0.92 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 88 TYR 0.010 0.001 TYR H 669 PHE 0.014 0.002 PHE F 111 TRP 0.006 0.001 TRP H 277 HIS 0.009 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (12546) covalent geometry : angle 0.67683 / 0.39 (17713) hydrogen bonds : bond 0.04625 / 4.94 ( 573) hydrogen bonds : angle 4.85327 / 6.61 ( 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 125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8536 (tm-30) REVERT: F 40 GLU cc_start: 0.8347 (tp30) cc_final: 0.8087 (tp30) REVERT: F 80 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8165 (mm-40) REVERT: G 93 LYS cc_start: 0.5265 (tttt) cc_final: 0.3911 (mttm) REVERT: G 111 PHE cc_start: 0.6480 (t80) cc_final: 0.6150 (t80) REVERT: E 40 GLU cc_start: 0.8065 (tp30) cc_final: 0.7812 (tp30) REVERT: H 2 MET cc_start: 0.6209 (mtp) cc_final: 0.5700 (mtp) REVERT: H 223 MET cc_start: 0.4566 (mmm) cc_final: 0.3885 (mmm) REVERT: H 566 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.4900 (mtm-85) outliers start: 16 outliers final: 6 residues processed: 122 average time/residue: 0.0939 time to fit residues: 17.2919 Evaluate side-chains 100 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 700 SER 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: 0.6980 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.081377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.064839 restraints weight = 56824.438| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.97 r_work: 0.3259 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12546 Z= 0.195 Angle : 0.680 12.838 17713 Z= 0.386 Chirality : 0.044 0.304 1982 Planarity : 0.005 0.050 1654 Dihedral : 27.880 167.718 3238 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.82 % Allowed : 13.15 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.26), residues: 1031 helix: 0.66 (0.24), residues: 445 sheet: -0.58 (0.35), residues: 212 loop : -0.84 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 57 TYR 0.010 0.001 TYR H 213 PHE 0.030 0.002 PHE F 111 TRP 0.006 0.001 TRP H 172 HIS 0.006 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (12546) covalent geometry : angle 0.67995 / 0.39 (17713) hydrogen bonds : bond 0.04789 / 5.13 ( 573) hydrogen bonds : angle 4.74851 / 6.46 ( 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 126 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8671 (tm-30) REVERT: F 40 GLU cc_start: 0.8360 (tp30) cc_final: 0.8150 (tp30) REVERT: F 80 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8162 (mm-40) REVERT: F 111 PHE cc_start: 0.6289 (t80) cc_final: 0.5791 (t80) REVERT: G 93 LYS cc_start: 0.5399 (tttt) cc_final: 0.3964 (mttm) REVERT: G 111 PHE cc_start: 0.6591 (t80) cc_final: 0.6363 (t80) REVERT: E 40 GLU cc_start: 0.8100 (tp30) cc_final: 0.7897 (tp30) REVERT: H 2 MET cc_start: 0.6198 (mtp) cc_final: 0.5962 (mtp) REVERT: H 223 MET cc_start: 0.4638 (mmm) cc_final: 0.4219 (mmm) REVERT: H 810 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7214 (ptt180) outliers start: 24 outliers final: 14 residues processed: 124 average time/residue: 0.0846 time to fit residues: 16.1458 Evaluate side-chains 108 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 25 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.081727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.064647 restraints weight = 56897.993| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.37 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12546 Z= 0.166 Angle : 0.654 12.180 17713 Z= 0.372 Chirality : 0.043 0.287 1982 Planarity : 0.004 0.049 1654 Dihedral : 27.846 167.374 3238 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.58 % Allowed : 14.44 % Favored : 82.98 % 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: -0.17 (0.26), residues: 1031 helix: 0.83 (0.24), residues: 442 sheet: -0.70 (0.33), residues: 226 loop : -0.74 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 118 TYR 0.015 0.001 TYR H 200 PHE 0.021 0.002 PHE F 111 TRP 0.005 0.001 TRP H 277 HIS 0.004 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (12546) covalent geometry : angle 0.65371 / 0.37 (17713) hydrogen bonds : bond 0.04260 / 4.50 ( 573) hydrogen bonds : angle 4.65644 / 6.33 ( 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 121 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8524 (tm-30) REVERT: F 80 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7986 (mm-40) REVERT: G 93 LYS cc_start: 0.5420 (tttt) cc_final: 0.4055 (mttm) REVERT: G 111 PHE cc_start: 0.6406 (t80) cc_final: 0.6178 (t80) REVERT: E 40 GLU cc_start: 0.7643 (tp30) cc_final: 0.7414 (tp30) REVERT: H 223 MET cc_start: 0.4874 (mmm) cc_final: 0.4110 (mmm) REVERT: H 566 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.4756 (mtm-85) REVERT: H 810 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7191 (ptt180) outliers start: 22 outliers final: 15 residues processed: 118 average time/residue: 0.0917 time to fit residues: 16.2934 Evaluate side-chains 114 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 2.9990 chunk 27 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.081747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.065209 restraints weight = 57328.239| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.84 r_work: 0.3295 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12546 Z= 0.159 Angle : 0.641 11.529 17713 Z= 0.365 Chirality : 0.042 0.277 1982 Planarity : 0.004 0.048 1654 Dihedral : 27.825 165.802 3238 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.40 % Allowed : 14.20 % 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: -0.08 (0.26), residues: 1031 helix: 0.96 (0.24), residues: 444 sheet: -0.69 (0.33), residues: 225 loop : -0.75 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 57 TYR 0.012 0.001 TYR H 200 PHE 0.031 0.002 PHE F 111 TRP 0.005 0.001 TRP H 172 HIS 0.004 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (12546) covalent geometry : angle 0.64068 / 0.37 (17713) hydrogen bonds : bond 0.04167 / 4.41 ( 573) hydrogen bonds : angle 4.54547 / 6.13 ( 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 129 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8571 (tm-30) REVERT: F 80 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8105 (mm-40) REVERT: G 81 LEU cc_start: 0.3723 (OUTLIER) cc_final: 0.3481 (mm) REVERT: G 93 LYS cc_start: 0.5350 (tttt) cc_final: 0.4138 (mttm) REVERT: G 111 PHE cc_start: 0.6654 (t80) cc_final: 0.6306 (t80) REVERT: E 40 GLU cc_start: 0.7995 (tp30) cc_final: 0.7749 (tp30) REVERT: H 223 MET cc_start: 0.4628 (mmm) cc_final: 0.3885 (mmm) REVERT: H 566 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.4889 (mtm-85) REVERT: H 810 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7037 (ptt180) outliers start: 29 outliers final: 16 residues processed: 125 average time/residue: 0.0891 time to fit residues: 17.0176 Evaluate side-chains 111 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 66 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain E residue 13 MET 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 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: 0.5980 chunk 26 optimal weight: 0.2980 chunk 94 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.081924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063505 restraints weight = 56865.496| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.81 r_work: 0.3323 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12546 Z= 0.155 Angle : 0.653 14.013 17713 Z= 0.366 Chirality : 0.042 0.423 1982 Planarity : 0.004 0.049 1654 Dihedral : 27.782 164.678 3238 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.17 % Allowed : 15.73 % 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: -0.09 (0.26), residues: 1031 helix: 0.92 (0.24), residues: 447 sheet: -0.64 (0.33), residues: 225 loop : -0.75 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 100 TYR 0.012 0.001 TYR H 200 PHE 0.033 0.002 PHE F 111 TRP 0.007 0.001 TRP H 277 HIS 0.004 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (12546) covalent geometry : angle 0.65304 / 0.37 (17713) hydrogen bonds : bond 0.04118 / 4.35 ( 573) hydrogen bonds : angle 4.52757 / 6.12 ( 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 127 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8576 (tm-30) REVERT: F 40 GLU cc_start: 0.8597 (tp30) cc_final: 0.8122 (tp30) REVERT: F 80 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8126 (mm-40) REVERT: G 37 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7470 (mmt-90) REVERT: G 81 LEU cc_start: 0.3723 (OUTLIER) cc_final: 0.3462 (mm) REVERT: G 93 LYS cc_start: 0.5245 (tttt) cc_final: 0.4059 (mttm) REVERT: G 111 PHE cc_start: 0.6629 (t80) cc_final: 0.6299 (t80) REVERT: E 40 GLU cc_start: 0.7949 (tp30) cc_final: 0.7695 (tp30) REVERT: H 106 HIS cc_start: 0.6624 (OUTLIER) cc_final: 0.5560 (t-90) REVERT: H 223 MET cc_start: 0.4626 (mmm) cc_final: 0.3893 (mmm) REVERT: H 810 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7000 (ptt180) outliers start: 27 outliers final: 22 residues processed: 124 average time/residue: 0.0777 time to fit residues: 14.8337 Evaluate side-chains 121 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 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 106 HIS Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 569 THR Chi-restraints excluded: chain H residue 663 THR Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 724 ILE 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: 3.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 94 optimal weight: 0.0030 chunk 12 optimal weight: 8.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 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 = 0.3970 r_free = 0.3970 target = 0.082107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.063734 restraints weight = 56505.188| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.79 r_work: 0.3333 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3212 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= 0.148 Angle : 0.644 12.601 17713 Z= 0.364 Chirality : 0.041 0.336 1982 Planarity : 0.004 0.048 1654 Dihedral : 27.711 163.404 3238 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.93 % Allowed : 15.96 % 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: 0.01 (0.27), residues: 1031 helix: 0.97 (0.25), residues: 448 sheet: -0.56 (0.34), residues: 216 loop : -0.70 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 32 TYR 0.012 0.001 TYR H 200 PHE 0.019 0.002 PHE F 111 TRP 0.007 0.001 TRP H 277 HIS 0.005 0.001 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (12546) covalent geometry : angle 0.64410 / 0.36 (17713) hydrogen bonds : bond 0.04044 / 4.26 ( 573) hydrogen bonds : angle 4.42123 / 5.91 ( 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 125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8575 (tm-30) REVERT: G 13 MET cc_start: 0.7538 (tpt) cc_final: 0.7319 (tpt) REVERT: G 37 ARG cc_start: 0.8008 (mmt180) cc_final: 0.7565 (mmt-90) REVERT: G 81 LEU cc_start: 0.3678 (OUTLIER) cc_final: 0.3435 (mm) REVERT: G 93 LYS cc_start: 0.5238 (tttt) cc_final: 0.4061 (mttm) REVERT: G 111 PHE cc_start: 0.6685 (t80) cc_final: 0.6321 (t80) REVERT: E 40 GLU cc_start: 0.7981 (tp30) cc_final: 0.7710 (tp30) REVERT: H 106 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.5621 (t-90) REVERT: H 144 PHE cc_start: 0.7143 (m-80) cc_final: 0.6893 (m-80) REVERT: H 223 MET cc_start: 0.4538 (mmm) cc_final: 0.4068 (mmm) REVERT: H 566 ARG cc_start: 0.5903 (OUTLIER) cc_final: 0.4867 (mtm-85) REVERT: H 810 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6903 (ptt180) outliers start: 25 outliers final: 18 residues processed: 121 average time/residue: 0.0980 time to fit residues: 17.6986 Evaluate side-chains 117 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 D residue 60 THR Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 87 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 106 HIS 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 663 THR 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: 1.9990 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.081695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063391 restraints weight = 56540.490| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.77 r_work: 0.3323 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12546 Z= 0.163 Angle : 0.657 13.168 17713 Z= 0.369 Chirality : 0.042 0.367 1982 Planarity : 0.004 0.059 1654 Dihedral : 27.717 162.047 3238 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: -0.04 (0.26), residues: 1031 helix: 0.92 (0.24), residues: 449 sheet: -0.66 (0.33), residues: 217 loop : -0.65 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 44 TYR 0.010 0.001 TYR H 200 PHE 0.019 0.002 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 0.00314 / 0.16 (12546) covalent geometry : angle 0.65721 / 0.37 (17713) hydrogen bonds : bond 0.04220 / 4.47 ( 573) hydrogen bonds : angle 4.49046 / 6.07 ( 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 123 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8546 (tm-30) REVERT: G 13 MET cc_start: 0.7571 (tpt) cc_final: 0.7318 (tpt) REVERT: G 37 ARG cc_start: 0.8041 (mmt180) cc_final: 0.7609 (mmt-90) REVERT: G 81 LEU cc_start: 0.3703 (OUTLIER) cc_final: 0.3456 (mm) REVERT: G 93 LYS cc_start: 0.5267 (tttt) cc_final: 0.4078 (mttm) REVERT: G 111 PHE cc_start: 0.6705 (t80) cc_final: 0.6307 (t80) REVERT: E 40 GLU cc_start: 0.7966 (tp30) cc_final: 0.7709 (tp30) REVERT: H 106 HIS cc_start: 0.6621 (OUTLIER) cc_final: 0.5646 (t-90) REVERT: H 223 MET cc_start: 0.4392 (mmm) cc_final: 0.3972 (mmm) REVERT: H 566 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.4850 (mtm-85) REVERT: H 754 GLU cc_start: 0.8652 (pt0) cc_final: 0.8447 (mp0) REVERT: H 810 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6922 (ptt180) outliers start: 24 outliers final: 18 residues processed: 121 average time/residue: 0.0855 time to fit residues: 15.7483 Evaluate side-chains 113 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 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 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 106 HIS 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 663 THR Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 810 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 0.2980 chunk 91 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.082306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.065890 restraints weight = 56984.032| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.85 r_work: 0.3318 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12546 Z= 0.140 Angle : 0.641 13.828 17713 Z= 0.362 Chirality : 0.040 0.228 1982 Planarity : 0.004 0.045 1654 Dihedral : 27.644 161.078 3238 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.23 % Allowed : 16.90 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.27), residues: 1031 helix: 0.95 (0.25), residues: 449 sheet: -0.65 (0.33), residues: 226 loop : -0.65 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 615 TYR 0.011 0.001 TYR H 200 PHE 0.013 0.001 PHE F 108 TRP 0.022 0.001 TRP H 774 HIS 0.005 0.001 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (12546) covalent geometry : angle 0.64125 / 0.36 (17713) hydrogen bonds : bond 0.03887 / 4.10 ( 573) hydrogen bonds : angle 4.45371 / 6.00 ( 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 119 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 23 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8539 (tm-30) REVERT: G 37 ARG cc_start: 0.8058 (mmt180) cc_final: 0.7673 (mmt-90) REVERT: G 45 LEU cc_start: 0.6876 (tp) cc_final: 0.6564 (mm) REVERT: G 52 TYR cc_start: 0.4393 (m-80) cc_final: 0.4106 (m-80) REVERT: G 81 LEU cc_start: 0.3689 (OUTLIER) cc_final: 0.3451 (mm) REVERT: G 93 LYS cc_start: 0.5330 (tttt) cc_final: 0.4086 (mttm) REVERT: G 111 PHE cc_start: 0.6763 (t80) cc_final: 0.6392 (t80) REVERT: E 40 GLU cc_start: 0.7929 (tp30) cc_final: 0.7670 (tp30) REVERT: H 106 HIS cc_start: 0.6569 (OUTLIER) cc_final: 0.5706 (t-90) REVERT: H 223 MET cc_start: 0.4377 (mmm) cc_final: 0.3935 (mmm) REVERT: H 566 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.4887 (mtm-85) REVERT: H 754 GLU cc_start: 0.8647 (pt0) cc_final: 0.8431 (mp0) outliers start: 19 outliers final: 15 residues processed: 118 average time/residue: 0.1007 time to fit residues: 17.8865 Evaluate side-chains 114 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR 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 87 ASN Chi-restraints excluded: chain F residue 101 VAL 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 106 HIS 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 663 THR 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: 0.5980 chunk 52 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN 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 = 0.082213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.065611 restraints weight = 56383.743| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.86 r_work: 0.3313 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12546 Z= 0.148 Angle : 0.644 13.769 17713 Z= 0.363 Chirality : 0.040 0.221 1982 Planarity : 0.004 0.053 1654 Dihedral : 27.633 159.427 3238 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.58 % Allowed : 17.37 % Favored : 80.05 % 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 (0.27), residues: 1031 helix: 0.96 (0.24), residues: 449 sheet: -0.78 (0.33), residues: 224 loop : -0.57 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.010 0.001 TYR H 200 PHE 0.018 0.001 PHE F 111 TRP 0.066 0.002 TRP H 774 HIS 0.004 0.001 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (12546) covalent geometry : angle 0.64400 / 0.36 (17713) hydrogen bonds : bond 0.03959 / 4.19 ( 573) hydrogen bonds : angle 4.44546 / 6.01 ( 1474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3029.00 seconds wall clock time: 52 minutes 33.38 seconds (3153.38 seconds total)