Starting phenix.real_space_refine on Wed Aug 5 20:59:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f11_50121/08_2026/9f11_50121.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f11_50121/08_2026/9f11_50121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f11_50121/08_2026/9f11_50121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f11_50121/08_2026/9f11_50121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f11_50121/08_2026/9f11_50121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f11_50121/08_2026/9f11_50121.map" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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 32 5.16 5 C 6911 2.51 5 N 2172 2.21 5 O 2653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 11950 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: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "F" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 958 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 787 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 3, 'TYR:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "H" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4053 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 21, 'TRANS': 521} Chain breaks: 7 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 8, 'ASP:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 4, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 107 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: 1.75, per 1000 atoms: 0.15 Number of scatterers: 11950 At special positions: 0 Unit cell: (94.05, 130.35, 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 32 16.00 P 181 15.00 Mg 1 11.99 O 2653 8.00 N 2172 7.00 C 6911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 291.4 milliseconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 13 sheets defined 45.4% alpha, 17.5% beta 75 base pairs and 156 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.574A pdb=" N ILE C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'D' and resid 2 through 14 removed outlier: 3.513A pdb=" N GLU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 39 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'E' and resid 20 through 34 removed outlier: 3.881A pdb=" N SER E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.536A pdb=" N ALA E 41 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP E 47 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 90 Processing helix chain 'E' and resid 92 through 108 Processing helix chain 'F' and resid 20 through 34 removed outlier: 3.750A pdb=" N SER F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 52 Processing helix chain 'F' and resid 75 through 90 Processing helix chain 'F' and resid 92 through 108 removed outlier: 3.607A pdb=" N ASP F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 34 removed outlier: 4.035A pdb=" N SER G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU G 26 " --> pdb=" O VAL G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 52 removed outlier: 3.809A pdb=" N HIS G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR G 52 " --> pdb=" O HIS G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 92 through 108 Processing helix chain 'H' and resid 11 through 15 removed outlier: 3.676A pdb=" N GLY H 14 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN H 15 " --> pdb=" O SER H 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 11 through 15' Processing helix chain 'H' and resid 35 through 42 Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 87 through 98 Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 102 through 118 removed outlier: 3.757A pdb=" N GLN H 116 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 192 Processing helix chain 'H' and resid 192 through 211 removed outlier: 3.516A pdb=" N LYS H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN H 207 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 234 Processing helix chain 'H' and resid 235 through 246 Processing helix chain 'H' and resid 251 through 262 Processing helix chain 'H' and resid 271 through 285 Processing helix chain 'H' and resid 287 through 298 removed outlier: 3.767A pdb=" N TYR H 291 " --> pdb=" O ASP H 287 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG H 292 " --> pdb=" O ILE H 288 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP H 293 " --> pdb=" O ARG H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 576 through 594 Processing helix chain 'H' and resid 603 through 621 removed outlier: 3.549A pdb=" N ALA H 608 " --> pdb=" O VAL H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 646 through 650 removed outlier: 3.511A 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 798 through 808 removed outlier: 3.509A pdb=" N SER H 808 " --> pdb=" O GLY H 804 " (cutoff:3.500A) Processing helix chain 'H' and resid 822 through 827 Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46 removed outlier: 3.679A 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 'D' and resid 59 through 62 Processing sheet with id=AA4, first strand: chain 'E' and resid 13 through 19 Processing sheet with id=AA5, first strand: chain 'F' and resid 13 through 19 Processing sheet with id=AA6, first strand: chain 'G' and resid 14 through 19 Processing sheet with id=AA7, first strand: chain 'H' and resid 2 through 7 removed outlier: 4.515A pdb=" N GLY H 79 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL H 161 " --> pdb=" O ALA H 142 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL H 140 " --> pdb=" O ALA H 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AA9, first strand: chain 'H' and resid 122 through 126 Processing sheet with id=AB1, first strand: chain 'H' and resid 216 through 219 removed outlier: 6.818A pdb=" N MET H 223 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 568 through 572 removed outlier: 6.744A pdb=" N VAL H 788 " --> pdb=" O ARG H 813 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR H 815 " --> pdb=" O VAL H 788 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA H 790 " --> pdb=" O TYR H 815 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL H 598 " --> pdb=" O PHE H 789 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N SER H 791 " --> pdb=" O VAL H 598 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN H 600 " --> pdb=" O SER H 791 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N GLU H 776 " --> pdb=" O SER H 597 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA H 599 " --> pdb=" O GLU H 776 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 629 through 636 removed outlier: 6.660A pdb=" N THR H 682 " --> pdb=" O ASP H 672 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL H 674 " --> pdb=" O SER H 680 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER H 680 " --> pdb=" O VAL H 674 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 755 through 759 removed outlier: 6.647A pdb=" N VAL H 748 " --> pdb=" O VAL H 737 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL H 737 " --> pdb=" O VAL H 748 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 169 hydrogen bonds 334 hydrogen bond angles 0 basepair planarities 75 basepair parallelities 156 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 0.87 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: 2588 1.33 - 1.45: 3397 1.45 - 1.57: 6124 1.57 - 1.69: 360 1.69 - 1.81: 61 Bond restraints: 12530 Sorted by residual: bond pdb=" C3' DA B 88 " pdb=" C2' DA B 88 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DA B 64 " pdb=" O3' DA B 64 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.08e+01 bond pdb=" C3' DT A 60 " pdb=" O3' DT A 60 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" C3' DT A 61 " pdb=" C2' DT A 61 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG A 79 " pdb=" C2' DG A 79 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 12525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 17087 2.14 - 4.29: 574 4.29 - 6.43: 32 6.43 - 8.57: 7 8.57 - 10.71: 4 Bond angle restraints: 17704 Sorted by residual: angle pdb=" O4' DA B 44 " pdb=" C4' DA B 44 " pdb=" C3' DA B 44 " ideal model delta sigma weight residual 106.00 102.23 3.77 6.00e-01 2.78e+00 3.96e+01 angle pdb=" C3' DG A 9 " pdb=" O3' DG A 9 " pdb=" P DT A 8 " ideal model delta sigma weight residual 119.70 127.16 -7.46 1.20e+00 6.94e-01 3.86e+01 angle pdb=" O4' DT A 46 " pdb=" C4' DT A 46 " pdb=" C3' DT A 46 " ideal model delta sigma weight residual 106.00 102.80 3.20 6.00e-01 2.78e+00 2.85e+01 angle pdb=" C3' DT B 82 " pdb=" O3' DT B 82 " pdb=" P DA B 83 " ideal model delta sigma weight residual 119.70 125.80 -6.10 1.20e+00 6.94e-01 2.59e+01 angle pdb=" O4' DA A 81 " pdb=" C4' DA A 81 " pdb=" C3' DA A 81 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.49e+01 ... (remaining 17699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 6342 35.09 - 70.18: 828 70.18 - 105.27: 12 105.27 - 140.36: 1 140.36 - 175.45: 3 Dihedral angle restraints: 7186 sinusoidal: 4122 harmonic: 3064 Sorted by residual: dihedral pdb=" CA THR F 6 " pdb=" C THR F 6 " pdb=" N ARG F 7 " pdb=" CA ARG F 7 " ideal model delta harmonic sigma weight residual -180.00 -156.54 -23.46 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA PHE E 4 " pdb=" C PHE E 4 " pdb=" N GLY E 5 " pdb=" CA GLY E 5 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" C4' DG B 47 " pdb=" C3' DG B 47 " pdb=" O3' DG B 47 " pdb=" P DA B 48 " ideal model delta sinusoidal sigma weight residual 220.00 44.55 175.45 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1932 0.113 - 0.226: 46 0.226 - 0.339: 0 0.339 - 0.452: 2 0.452 - 0.565: 8 Chirality restraints: 1988 Sorted by residual: chirality pdb=" P DA B 83 " pdb=" OP1 DA B 83 " pdb=" OP2 DA B 83 " pdb=" O5' DA B 83 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 7.99e+00 chirality pdb=" P DT A 8 " pdb=" OP1 DT A 8 " pdb=" OP2 DT A 8 " pdb=" O5' DT A 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.82e+00 chirality pdb=" P DG A 7 " pdb=" OP1 DG A 7 " pdb=" OP2 DG A 7 " pdb=" O5' DG A 7 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.52e+00 ... (remaining 1985 not shown) Planarity restraints: 1651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT A 46 " -0.026 2.00e-02 2.50e+03 1.23e-02 3.79e+00 pdb=" N1 DT A 46 " 0.025 2.00e-02 2.50e+03 pdb=" C2 DT A 46 " 0.000 2.00e-02 2.50e+03 pdb=" O2 DT A 46 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT A 46 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DT A 46 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT A 46 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DT A 46 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT A 46 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT A 46 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA A 21 " 0.024 2.00e-02 2.50e+03 1.07e-02 3.16e+00 pdb=" N9 DA A 21 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA A 21 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DA A 21 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA A 21 " -0.002 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 " 0.000 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 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT A 13 " 0.022 2.00e-02 2.50e+03 1.09e-02 2.98e+00 pdb=" N1 DT A 13 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DT A 13 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT A 13 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT A 13 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT A 13 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT A 13 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT A 13 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT A 13 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT A 13 " -0.003 2.00e-02 2.50e+03 ... (remaining 1648 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 36 2.43 - 3.05: 7148 3.05 - 3.67: 19354 3.67 - 4.28: 29150 4.28 - 4.90: 43934 Nonbonded interactions: 99622 Sorted by model distance: nonbonded pdb=" OP1 DG A -1 " pdb="MG MG H1801 " model vdw 1.813 2.170 nonbonded pdb=" NE2 HIS H 157 " pdb="MG MG H1801 " model vdw 1.890 2.250 nonbonded pdb=" ND1 HIS H 146 " pdb="MG MG H1801 " model vdw 1.962 2.250 nonbonded pdb=" OG SER E 30 " pdb=" O ARG E 35 " model vdw 2.180 3.040 nonbonded pdb=" OE2 GLU H 209 " pdb=" OG1 THR H 215 " model vdw 2.213 3.040 ... (remaining 99617 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 12 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or (resid 62 and (name N or \ name CA or name C or name O or name CB )) or resid 63 or (resid 64 and (name N o \ r name CA or name C or name O or name CB )) or resid 65 through 68 or (resid 69 \ and (name N or name CA or name C or name O or name CB )) or resid 70 through 72 \ or (resid 73 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 4 through 95 or (resid 96 through 98 and (name N or name CA or name C or name O \ or name CB )) or resid 99 through 106 or (resid 107 through 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 110 or (resid 111 \ and (name N or name CA or name C or name O or name CB )) or resid 112 through 11 \ 3)) selection = (chain 'F' and (resid 12 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or (resid 62 and (name N or \ name CA or name C or name O or name CB )) or resid 63 through 68 or (resid 69 an \ d (name N or name CA or name C or name O or name CB )) or resid 70 through 72 or \ (resid 73 and (name N or name CA or name C or name O or name CB )) or resid 74 \ through 95 or (resid 96 through 98 and (name N or name CA or name C or name O or \ name CB )) or resid 99 through 106 or (resid 107 through 108 and (name N or nam \ e CA or name C or name O or name CB )) or resid 109 through 110 or (resid 111 an \ d (name N or name CA or name C or name O or name CB )) or resid 112 through 113) \ ) selection = (chain 'G' and resid 12 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.620 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.000 Find NCS groups from input model: 0.060 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.006 0.043 12530 Z= 0.489 Angle : 0.785 10.715 17704 Z= 0.639 Chirality : 0.057 0.565 1988 Planarity : 0.004 0.036 1651 Dihedral : 23.271 175.445 5198 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.23 % Allowed : 2.20 % Favored : 97.56 % 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 (0.25), residues: 1039 helix: 0.60 (0.24), residues: 451 sheet: -0.55 (0.36), residues: 202 loop : -0.42 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 63 TYR 0.011 0.001 TYR H 669 PHE 0.010 0.001 PHE E 55 TRP 0.006 0.001 TRP H 224 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.49 (12530) covalent geometry : angle 0.78505 / 0.64 (17704) hydrogen bonds : bond 0.17539 / 20.17 ( 593) hydrogen bonds : angle 6.88021 / 8.73 ( 1561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 THR cc_start: 0.8253 (t) cc_final: 0.7763 (t) REVERT: D 50 SER cc_start: 0.8943 (p) cc_final: 0.8743 (m) REVERT: D 68 ASP cc_start: 0.7807 (m-30) cc_final: 0.7594 (t70) REVERT: F 43 ILE cc_start: 0.8981 (mt) cc_final: 0.8710 (mt) REVERT: G 14 VAL cc_start: 0.8569 (t) cc_final: 0.8365 (m) REVERT: G 31 ASN cc_start: 0.8033 (m-40) cc_final: 0.7767 (m-40) REVERT: G 39 PHE cc_start: 0.8321 (t80) cc_final: 0.7755 (t80) REVERT: G 102 ILE cc_start: 0.9156 (mt) cc_final: 0.8853 (tp) REVERT: H 1 MET cc_start: 0.7250 (tpt) cc_final: 0.6940 (tpp) REVERT: H 2 MET cc_start: 0.7662 (ttt) cc_final: 0.7411 (ttp) REVERT: H 95 MET cc_start: 0.6253 (mmt) cc_final: 0.5946 (mtt) outliers start: 2 outliers final: 1 residues processed: 272 average time/residue: 0.1010 time to fit residues: 38.1076 Evaluate side-chains 119 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 158 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 ASN H 6 GLN H 221 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.081333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.061417 restraints weight = 48183.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063010 restraints weight = 25534.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.064013 restraints weight = 17268.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064645 restraints weight = 13570.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.065036 restraints weight = 11729.067| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12530 Z= 0.186 Angle : 0.741 10.964 17704 Z= 0.419 Chirality : 0.047 0.323 1988 Planarity : 0.005 0.050 1651 Dihedral : 27.919 176.695 3232 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.74 % Allowed : 13.11 % Favored : 85.15 % 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 (0.25), residues: 1039 helix: 0.80 (0.23), residues: 464 sheet: -0.45 (0.35), residues: 208 loop : -0.42 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 810 TYR 0.018 0.002 TYR G 52 PHE 0.014 0.002 PHE C 13 TRP 0.011 0.001 TRP F 91 HIS 0.010 0.001 HIS H 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.19 (12530) covalent geometry : angle 0.74052 / 0.42 (17704) hydrogen bonds : bond 0.05532 / 6.01 ( 593) hydrogen bonds : angle 5.10062 / 6.38 ( 1561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8053 (m-30) cc_final: 0.7637 (t70) REVERT: E 16 LEU cc_start: 0.8396 (tp) cc_final: 0.8181 (tp) REVERT: F 39 PHE cc_start: 0.8917 (t80) cc_final: 0.8504 (t80) REVERT: G 31 ASN cc_start: 0.8242 (m-40) cc_final: 0.7797 (m-40) REVERT: G 42 VAL cc_start: 0.8672 (t) cc_final: 0.8410 (t) REVERT: H 1 MET cc_start: 0.7017 (tpt) cc_final: 0.6816 (tpt) REVERT: H 2 MET cc_start: 0.7516 (ttt) cc_final: 0.7004 (ttp) REVERT: H 95 MET cc_start: 0.6360 (mmt) cc_final: 0.5657 (mtp) REVERT: H 190 TYR cc_start: 0.8317 (m-80) cc_final: 0.7759 (m-80) outliers start: 15 outliers final: 13 residues processed: 149 average time/residue: 0.0736 time to fit residues: 16.9449 Evaluate side-chains 127 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 590 SER Chi-restraints excluded: chain H residue 626 LEU Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 746 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 9 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 0.0470 chunk 12 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 1.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 13 GLN H 155 GLN H 612 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.079544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.059507 restraints weight = 48642.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.060973 restraints weight = 26490.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061952 restraints weight = 18274.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.062528 restraints weight = 14442.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062933 restraints weight = 12522.688| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12530 Z= 0.234 Angle : 0.739 9.846 17704 Z= 0.413 Chirality : 0.047 0.317 1988 Planarity : 0.005 0.051 1651 Dihedral : 28.090 174.191 3232 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.90 % Allowed : 14.50 % Favored : 82.60 % 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: -0.10 (0.25), residues: 1039 helix: 0.78 (0.23), residues: 462 sheet: -0.83 (0.36), residues: 199 loop : -0.51 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 51 TYR 0.027 0.002 TYR G 52 PHE 0.026 0.003 PHE E 55 TRP 0.007 0.001 TRP H 224 HIS 0.005 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.23 (12530) covalent geometry : angle 0.73927 / 0.41 (17704) hydrogen bonds : bond 0.05092 / 5.40 ( 593) hydrogen bonds : angle 4.85923 / 6.10 ( 1561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7768 (t0) cc_final: 0.7486 (t0) REVERT: D 68 ASP cc_start: 0.8071 (m-30) cc_final: 0.7613 (t70) REVERT: G 31 ASN cc_start: 0.8189 (m-40) cc_final: 0.7749 (m-40) REVERT: G 42 VAL cc_start: 0.8676 (t) cc_final: 0.8238 (t) REVERT: H 1 MET cc_start: 0.7030 (tpt) cc_final: 0.6698 (tpt) REVERT: H 2 MET cc_start: 0.7561 (ttt) cc_final: 0.7013 (tmm) REVERT: H 95 MET cc_start: 0.6418 (mmt) cc_final: 0.5687 (mtt) REVERT: H 190 TYR cc_start: 0.8303 (m-80) cc_final: 0.7818 (m-80) REVERT: H 617 GLU cc_start: 0.7990 (tp30) cc_final: 0.7787 (tp30) outliers start: 25 outliers final: 21 residues processed: 136 average time/residue: 0.0969 time to fit residues: 19.9488 Evaluate side-chains 130 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 32 ARG Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 590 SER Chi-restraints excluded: chain H residue 626 LEU Chi-restraints excluded: chain H residue 629 VAL Chi-restraints excluded: chain H residue 649 MET Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 821 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 118 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 119 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.080309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.060373 restraints weight = 48654.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061918 restraints weight = 26377.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062896 restraints weight = 18015.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063473 restraints weight = 14226.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.063886 restraints weight = 12342.815| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12530 Z= 0.159 Angle : 0.653 7.791 17704 Z= 0.374 Chirality : 0.043 0.334 1988 Planarity : 0.004 0.045 1651 Dihedral : 27.968 175.224 3232 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.09 % Allowed : 15.55 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1039 helix: 1.07 (0.23), residues: 460 sheet: -0.72 (0.34), residues: 215 loop : -0.40 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 51 TYR 0.030 0.002 TYR G 52 PHE 0.017 0.002 PHE C 13 TRP 0.005 0.001 TRP H 774 HIS 0.005 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (12530) covalent geometry : angle 0.65302 / 0.37 (17704) hydrogen bonds : bond 0.04110 / 4.39 ( 593) hydrogen bonds : angle 4.58092 / 5.77 ( 1561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8029 (m-30) cc_final: 0.7610 (t70) REVERT: F 46 LYS cc_start: 0.9174 (ttpp) cc_final: 0.8899 (tppp) REVERT: G 31 ASN cc_start: 0.8208 (m-40) cc_final: 0.7767 (m-40) REVERT: H 1 MET cc_start: 0.7117 (tpt) cc_final: 0.6801 (tpt) REVERT: H 2 MET cc_start: 0.7565 (ttt) cc_final: 0.7031 (ttp) REVERT: H 95 MET cc_start: 0.6203 (mmt) cc_final: 0.5583 (mtt) REVERT: H 190 TYR cc_start: 0.8246 (m-80) cc_final: 0.7769 (m-80) REVERT: H 274 MET cc_start: 0.7469 (mmm) cc_final: 0.6921 (mmm) REVERT: H 278 MET cc_start: 0.8108 (mmm) cc_final: 0.7851 (mmt) outliers start: 18 outliers final: 16 residues processed: 130 average time/residue: 0.0847 time to fit residues: 17.2376 Evaluate side-chains 122 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 32 ARG Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 626 LEU Chi-restraints excluded: chain H residue 649 MET Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 747 VAL Chi-restraints excluded: chain H residue 821 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 35 optimal weight: 0.0770 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.082255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.062880 restraints weight = 48532.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064176 restraints weight = 27427.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.064646 restraints weight = 19283.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.064887 restraints weight = 15517.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.065027 restraints weight = 15408.193| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12530 Z= 0.150 Angle : 0.634 7.495 17704 Z= 0.364 Chirality : 0.042 0.329 1988 Planarity : 0.004 0.042 1651 Dihedral : 27.884 175.015 3232 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.67 % Allowed : 14.85 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1039 helix: 1.23 (0.24), residues: 460 sheet: -0.70 (0.34), residues: 215 loop : -0.42 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 810 TYR 0.033 0.002 TYR G 52 PHE 0.027 0.002 PHE H 16 TRP 0.011 0.001 TRP H 638 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (12530) covalent geometry : angle 0.63396 / 0.36 (17704) hydrogen bonds : bond 0.03933 / 4.19 ( 593) hydrogen bonds : angle 4.44044 / 5.57 ( 1561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 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: 23 poor density : 115 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8184 (ptp) cc_final: 0.7911 (ptm) REVERT: D 68 ASP cc_start: 0.8093 (m-30) cc_final: 0.7634 (t70) REVERT: F 46 LYS cc_start: 0.9135 (ttpp) cc_final: 0.8784 (tppp) REVERT: G 23 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7494 (mt-10) REVERT: G 31 ASN cc_start: 0.8192 (m-40) cc_final: 0.7784 (m-40) REVERT: G 37 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8087 (mtt180) REVERT: G 72 MET cc_start: 0.7732 (mmp) cc_final: 0.7508 (mmm) REVERT: H 1 MET cc_start: 0.7111 (tpt) cc_final: 0.6835 (tpt) REVERT: H 2 MET cc_start: 0.7536 (ttt) cc_final: 0.7132 (ttp) REVERT: H 95 MET cc_start: 0.6140 (mmt) cc_final: 0.5495 (mtt) REVERT: H 190 TYR cc_start: 0.8196 (m-80) cc_final: 0.7776 (m-80) REVERT: H 274 MET cc_start: 0.7410 (mmm) cc_final: 0.7188 (mmm) REVERT: H 278 MET cc_start: 0.8194 (mmm) cc_final: 0.7700 (mmt) outliers start: 23 outliers final: 16 residues processed: 130 average time/residue: 0.0970 time to fit residues: 18.9955 Evaluate side-chains 121 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 32 ARG Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 626 LEU Chi-restraints excluded: chain H residue 649 MET Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 821 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 10 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 48 HIS ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.079849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.059877 restraints weight = 49122.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061402 restraints weight = 26665.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062365 restraints weight = 18259.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062962 restraints weight = 14414.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.063372 restraints weight = 12462.349| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12530 Z= 0.176 Angle : 0.649 7.198 17704 Z= 0.370 Chirality : 0.042 0.328 1988 Planarity : 0.004 0.059 1651 Dihedral : 27.816 174.826 3232 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.25 % Allowed : 14.62 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1039 helix: 1.33 (0.24), residues: 460 sheet: -0.79 (0.34), residues: 217 loop : -0.49 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 77 TYR 0.020 0.002 TYR F 112 PHE 0.028 0.002 PHE H 16 TRP 0.009 0.001 TRP H 638 HIS 0.006 0.001 HIS G 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (12530) covalent geometry : angle 0.64902 / 0.37 (17704) hydrogen bonds : bond 0.04064 / 4.31 ( 593) hydrogen bonds : angle 4.40431 / 5.54 ( 1561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 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: 28 poor density : 110 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8301 (ptp) cc_final: 0.7932 (ptm) REVERT: D 68 ASP cc_start: 0.8044 (m-30) cc_final: 0.7656 (t70) REVERT: E 77 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8016 (tm-30) REVERT: F 46 LYS cc_start: 0.9150 (ttpp) cc_final: 0.8924 (tppp) REVERT: G 23 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7589 (mt-10) REVERT: G 31 ASN cc_start: 0.8180 (m-40) cc_final: 0.7789 (m-40) REVERT: H 1 MET cc_start: 0.7130 (tpt) cc_final: 0.6774 (tpt) REVERT: H 2 MET cc_start: 0.7610 (ttt) cc_final: 0.7222 (ttp) REVERT: H 95 MET cc_start: 0.6090 (mmt) cc_final: 0.5379 (mtm) REVERT: H 190 TYR cc_start: 0.8294 (m-80) cc_final: 0.7818 (m-80) REVERT: H 274 MET cc_start: 0.7449 (mmm) cc_final: 0.7201 (mmm) REVERT: H 278 MET cc_start: 0.8148 (mmm) cc_final: 0.7677 (mmt) outliers start: 28 outliers final: 20 residues processed: 128 average time/residue: 0.0888 time to fit residues: 17.6476 Evaluate side-chains 121 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 32 ARG Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 590 SER Chi-restraints excluded: chain H residue 626 LEU Chi-restraints excluded: chain H residue 649 MET Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 821 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 16 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 HIS ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.078505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.058564 restraints weight = 48955.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059980 restraints weight = 27631.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.060884 restraints weight = 19328.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.061437 restraints weight = 15440.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.061809 restraints weight = 13466.260| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12530 Z= 0.243 Angle : 0.724 8.136 17704 Z= 0.403 Chirality : 0.045 0.325 1988 Planarity : 0.005 0.039 1651 Dihedral : 27.936 174.908 3232 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.48 % Allowed : 14.39 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1039 helix: 1.14 (0.24), residues: 462 sheet: -1.16 (0.36), residues: 201 loop : -0.60 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 51 TYR 0.018 0.002 TYR H 200 PHE 0.034 0.003 PHE H 16 TRP 0.009 0.002 TRP H 638 HIS 0.015 0.002 HIS G 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.24 (12530) covalent geometry : angle 0.72447 / 0.40 (17704) hydrogen bonds : bond 0.04726 / 5.02 ( 593) hydrogen bonds : angle 4.59282 / 5.79 ( 1561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8273 (ptp) cc_final: 0.8019 (ptm) REVERT: D 63 ASN cc_start: 0.7827 (t0) cc_final: 0.7591 (t0) REVERT: D 68 ASP cc_start: 0.8091 (m-30) cc_final: 0.7717 (t70) REVERT: F 46 LYS cc_start: 0.9167 (ttpp) cc_final: 0.8783 (tppp) REVERT: G 31 ASN cc_start: 0.8180 (m-40) cc_final: 0.7802 (m-40) REVERT: H 1 MET cc_start: 0.7097 (tpt) cc_final: 0.6708 (tpt) REVERT: H 2 MET cc_start: 0.7720 (ttt) cc_final: 0.7387 (ttp) REVERT: H 6 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: H 190 TYR cc_start: 0.8299 (m-80) cc_final: 0.7832 (m-80) outliers start: 30 outliers final: 24 residues processed: 120 average time/residue: 0.0852 time to fit residues: 16.0368 Evaluate side-chains 122 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 32 ARG Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 590 SER Chi-restraints excluded: chain H residue 626 LEU Chi-restraints excluded: chain H residue 649 MET Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 821 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN ** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.079828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059974 restraints weight = 48389.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061485 restraints weight = 26358.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.062441 restraints weight = 18044.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.063044 restraints weight = 14264.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.063368 restraints weight = 12346.246| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12530 Z= 0.148 Angle : 0.645 7.232 17704 Z= 0.369 Chirality : 0.042 0.340 1988 Planarity : 0.004 0.039 1651 Dihedral : 27.784 175.687 3232 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.32 % Allowed : 16.94 % Favored : 80.74 % 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: 0.21 (0.26), residues: 1039 helix: 1.33 (0.24), residues: 465 sheet: -0.92 (0.35), residues: 217 loop : -0.62 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 77 TYR 0.022 0.001 TYR F 112 PHE 0.035 0.002 PHE H 16 TRP 0.008 0.001 TRP H 638 HIS 0.012 0.001 HIS G 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (12530) covalent geometry : angle 0.64476 / 0.37 (17704) hydrogen bonds : bond 0.03862 / 4.11 ( 593) hydrogen bonds : angle 4.34808 / 5.51 ( 1561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 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: 20 poor density : 106 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8206 (ptp) cc_final: 0.7859 (ptm) REVERT: D 63 ASN cc_start: 0.7854 (t0) cc_final: 0.7555 (t0) REVERT: D 68 ASP cc_start: 0.8071 (m-30) cc_final: 0.7723 (t70) REVERT: E 95 ASP cc_start: 0.7885 (m-30) cc_final: 0.7241 (m-30) REVERT: F 46 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8814 (tppp) REVERT: G 31 ASN cc_start: 0.8207 (m-40) cc_final: 0.7833 (m-40) REVERT: G 37 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8108 (mtt180) REVERT: H 1 MET cc_start: 0.7205 (tpt) cc_final: 0.6840 (tpt) REVERT: H 2 MET cc_start: 0.7679 (ttt) cc_final: 0.7344 (ttp) REVERT: H 95 MET cc_start: 0.5879 (mmp) cc_final: 0.5651 (mmt) REVERT: H 190 TYR cc_start: 0.8165 (m-80) cc_final: 0.7772 (m-80) outliers start: 20 outliers final: 16 residues processed: 120 average time/residue: 0.0937 time to fit residues: 17.2905 Evaluate side-chains 118 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 32 ARG Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 626 LEU Chi-restraints excluded: chain H residue 649 MET Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 821 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 100 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 86 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 ASN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.081643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063297 restraints weight = 48542.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.063643 restraints weight = 30582.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.064123 restraints weight = 21008.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.064807 restraints weight = 19488.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.064866 restraints weight = 16626.506| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12530 Z= 0.150 Angle : 0.633 7.229 17704 Z= 0.361 Chirality : 0.041 0.329 1988 Planarity : 0.004 0.038 1651 Dihedral : 27.734 175.225 3232 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.86 % Allowed : 16.94 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1039 helix: 1.48 (0.24), residues: 465 sheet: -0.82 (0.35), residues: 218 loop : -0.53 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.014 0.001 TYR F 112 PHE 0.032 0.002 PHE H 16 TRP 0.009 0.001 TRP H 638 HIS 0.008 0.001 HIS G 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (12530) covalent geometry : angle 0.63293 / 0.36 (17704) hydrogen bonds : bond 0.03791 / 4.04 ( 593) hydrogen bonds : angle 4.23884 / 5.39 ( 1561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8099 (ptp) cc_final: 0.7854 (ptm) REVERT: D 68 ASP cc_start: 0.8055 (m-30) cc_final: 0.7746 (t70) REVERT: E 95 ASP cc_start: 0.7966 (m-30) cc_final: 0.7329 (m-30) REVERT: F 46 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8776 (tppp) REVERT: G 31 ASN cc_start: 0.8116 (m-40) cc_final: 0.7769 (m-40) REVERT: G 37 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8104 (mtt180) REVERT: G 72 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7295 (mmm) REVERT: H 1 MET cc_start: 0.7300 (tpt) cc_final: 0.6958 (tpt) REVERT: H 2 MET cc_start: 0.7671 (ttt) cc_final: 0.7465 (ttp) REVERT: H 190 TYR cc_start: 0.8083 (m-80) cc_final: 0.7804 (m-80) REVERT: H 278 MET cc_start: 0.7908 (mmp) cc_final: 0.7690 (mmm) outliers start: 16 outliers final: 14 residues processed: 116 average time/residue: 0.0831 time to fit residues: 15.1581 Evaluate side-chains 117 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 32 ARG Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 626 LEU Chi-restraints excluded: chain H residue 649 MET Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 821 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 52 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.079279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059332 restraints weight = 48769.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.060809 restraints weight = 26674.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061758 restraints weight = 18357.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.062362 restraints weight = 14548.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.062676 restraints weight = 12606.817| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12530 Z= 0.203 Angle : 0.667 7.316 17704 Z= 0.376 Chirality : 0.042 0.325 1988 Planarity : 0.004 0.038 1651 Dihedral : 27.818 175.006 3232 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.20 % Allowed : 16.47 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.26), residues: 1039 helix: 1.45 (0.24), residues: 465 sheet: -0.91 (0.35), residues: 222 loop : -0.55 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 668 TYR 0.016 0.002 TYR D 55 PHE 0.033 0.002 PHE H 16 TRP 0.008 0.001 TRP H 638 HIS 0.008 0.001 HIS G 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 (12530) covalent geometry : angle 0.66681 / 0.38 (17704) hydrogen bonds : bond 0.04147 / 4.38 ( 593) hydrogen bonds : angle 4.31073 / 5.47 ( 1561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8253 (ptp) cc_final: 0.7893 (ptm) REVERT: D 63 ASN cc_start: 0.7792 (t0) cc_final: 0.7519 (t0) REVERT: D 68 ASP cc_start: 0.8061 (m-30) cc_final: 0.7753 (t70) REVERT: E 95 ASP cc_start: 0.7936 (m-30) cc_final: 0.7309 (m-30) REVERT: F 46 LYS cc_start: 0.9155 (ttpp) cc_final: 0.8815 (tppp) REVERT: G 31 ASN cc_start: 0.8163 (m-40) cc_final: 0.7770 (m-40) REVERT: G 37 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8145 (mtt180) REVERT: H 1 MET cc_start: 0.7250 (tpt) cc_final: 0.6856 (tpt) REVERT: H 2 MET cc_start: 0.7712 (ttt) cc_final: 0.7421 (ttp) REVERT: H 95 MET cc_start: 0.5784 (mmp) cc_final: 0.5529 (mmt) REVERT: H 190 TYR cc_start: 0.8252 (m-80) cc_final: 0.7907 (m-80) REVERT: H 278 MET cc_start: 0.8011 (mmp) cc_final: 0.7758 (mmm) outliers start: 19 outliers final: 17 residues processed: 111 average time/residue: 0.0812 time to fit residues: 14.1352 Evaluate side-chains 117 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 32 ARG Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 626 LEU Chi-restraints excluded: chain H residue 649 MET Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 821 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 ASN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.079976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.060126 restraints weight = 48615.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.061635 restraints weight = 26405.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.062611 restraints weight = 18107.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.063207 restraints weight = 14285.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063536 restraints weight = 12373.845| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12530 Z= 0.154 Angle : 0.639 7.469 17704 Z= 0.364 Chirality : 0.041 0.333 1988 Planarity : 0.004 0.037 1651 Dihedral : 27.752 175.512 3232 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.09 % Allowed : 17.05 % Favored : 80.86 % 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: 0.44 (0.26), residues: 1039 helix: 1.51 (0.24), residues: 466 sheet: -0.77 (0.35), residues: 220 loop : -0.50 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 63 TYR 0.017 0.001 TYR F 112 PHE 0.038 0.002 PHE F 39 TRP 0.009 0.001 TRP H 638 HIS 0.006 0.001 HIS G 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (12530) covalent geometry : angle 0.63867 / 0.36 (17704) hydrogen bonds : bond 0.03791 / 4.00 ( 593) hydrogen bonds : angle 4.25396 / 5.41 ( 1561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.76 seconds wall clock time: 39 minutes 1.70 seconds (2341.70 seconds total)