Starting phenix.real_space_refine on Fri Jul 3 03:01:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f11_50121/07_2026/9f11_50121.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f11_50121/07_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_50121/07_2026/9f11_50121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f11_50121/07_2026/9f11_50121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f11_50121/07_2026/9f11_50121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f11_50121/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.77, per 1000 atoms: 0.23 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: 1.03 Conformation dependent library (CDL) restraints added in 566.4 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: 1.52 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: 2.80 Time building geometry restraints manager: 1.29 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: 17089 2.14 - 4.29: 574 4.29 - 6.43: 30 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=" 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=" 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 angle pdb=" C HIS H 168 " pdb=" CA HIS H 168 " pdb=" CB HIS H 168 " ideal model delta sigma weight residual 116.54 111.14 5.40 1.15e+00 7.56e-01 2.21e+01 angle pdb=" O3' DG A 9 " pdb=" P DT A 8 " pdb=" O5' DT A 8 " ideal model delta sigma weight residual 104.00 96.97 7.03 1.50e+00 4.44e-01 2.19e+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: 17.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.590 Find NCS groups from input model: 0.090 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.510 ------------------------------------------------------------------------------- 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= 0.488 Angle : 0.780 10.715 17704 Z= 0.634 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 0.77956 / 0.63 (17704) hydrogen bonds : bond 0.17539 / 20.08 ( 593) hydrogen bonds : angle 6.88021 / 8.71 ( 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 : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 50 SER cc_start: 0.8943 (p) cc_final: 0.8717 (m) REVERT: D 68 ASP cc_start: 0.7807 (m-30) cc_final: 0.7591 (t70) REVERT: F 43 ILE cc_start: 0.8981 (mt) cc_final: 0.8711 (mt) REVERT: G 14 VAL cc_start: 0.8569 (t) cc_final: 0.8366 (m) REVERT: G 31 ASN cc_start: 0.8033 (m-40) cc_final: 0.7756 (m-40) REVERT: G 39 PHE cc_start: 0.8321 (t80) cc_final: 0.7757 (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: 0.5945 (mtt) outliers start: 2 outliers final: 1 residues processed: 272 average time/residue: 0.1183 time to fit residues: 44.0370 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 : 0.384 ------------------------------------------------------------------------------- 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: 3.9990 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: 8.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 ASN H 6 GLN ** H 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.081262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.061388 restraints weight = 47957.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062952 restraints weight = 25480.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063850 restraints weight = 17304.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.064543 restraints weight = 13728.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.064894 restraints weight = 11852.034| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12530 Z= 0.183 Angle : 0.735 10.548 17704 Z= 0.417 Chirality : 0.046 0.302 1988 Planarity : 0.005 0.048 1651 Dihedral : 27.998 178.122 3232 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.62 % Allowed : 13.34 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1039 helix: 0.77 (0.23), residues: 464 sheet: -0.60 (0.37), residues: 190 loop : -0.48 (0.30), residues: 385 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 H 234 TRP 0.013 0.002 TRP F 91 HIS 0.013 0.001 HIS H 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 (12530) covalent geometry : angle 0.73479 / 0.42 (17704) hydrogen bonds : bond 0.05255 / 5.63 ( 593) hydrogen bonds : angle 5.04791 / 6.32 ( 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 151 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8070 (m-30) cc_final: 0.7636 (t70) REVERT: E 16 LEU cc_start: 0.8412 (tp) cc_final: 0.8200 (tp) REVERT: F 39 PHE cc_start: 0.8908 (t80) cc_final: 0.8542 (t80) REVERT: G 31 ASN cc_start: 0.8205 (m-40) cc_final: 0.7736 (m-40) REVERT: G 42 VAL cc_start: 0.8669 (t) cc_final: 0.8270 (t) REVERT: H 1 MET cc_start: 0.6963 (tpt) cc_final: 0.6755 (tpt) REVERT: H 2 MET cc_start: 0.7503 (ttt) cc_final: 0.6820 (tmm) REVERT: H 4 ILE cc_start: 0.8224 (mp) cc_final: 0.7891 (mp) REVERT: H 16 PHE cc_start: 0.6597 (t80) cc_final: 0.6374 (t80) REVERT: H 95 MET cc_start: 0.6360 (mmt) cc_final: 0.5655 (mtp) REVERT: H 190 TYR cc_start: 0.8301 (m-80) cc_final: 0.7767 (m-80) outliers start: 14 outliers final: 11 residues processed: 148 average time/residue: 0.0965 time to fit residues: 21.5476 Evaluate side-chains 125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 75 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 13 GLN E 56 ASN H 221 HIS H 612 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.080899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.062781 restraints weight = 48163.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.063308 restraints weight = 26324.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.063459 restraints weight = 19443.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.063799 restraints weight = 17413.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.063834 restraints weight = 15994.261| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12530 Z= 0.169 Angle : 0.670 8.964 17704 Z= 0.385 Chirality : 0.044 0.303 1988 Planarity : 0.004 0.052 1651 Dihedral : 28.013 174.936 3232 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.86 % Allowed : 14.73 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.25), residues: 1039 helix: 0.94 (0.23), residues: 464 sheet: -0.68 (0.35), residues: 198 loop : -0.46 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 810 TYR 0.023 0.002 TYR G 52 PHE 0.015 0.002 PHE C 13 TRP 0.005 0.001 TRP H 774 HIS 0.005 0.001 HIS F 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (12530) covalent geometry : angle 0.67023 / 0.39 (17704) hydrogen bonds : bond 0.04481 / 4.71 ( 593) hydrogen bonds : angle 4.69167 / 5.88 ( 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 141 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7653 (t0) cc_final: 0.7067 (m-40) REVERT: D 68 ASP cc_start: 0.8174 (m-30) cc_final: 0.7621 (t70) REVERT: G 23 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7529 (mt-10) REVERT: G 31 ASN cc_start: 0.8150 (m-40) cc_final: 0.7700 (m-40) REVERT: G 72 MET cc_start: 0.7847 (mmp) cc_final: 0.7498 (mmm) REVERT: H 1 MET cc_start: 0.7149 (tpt) cc_final: 0.6904 (tpt) REVERT: H 2 MET cc_start: 0.7465 (ttt) cc_final: 0.6732 (tmm) REVERT: H 4 ILE cc_start: 0.8310 (mp) cc_final: 0.7916 (mp) REVERT: H 95 MET cc_start: 0.6462 (mmt) cc_final: 0.5831 (mtt) REVERT: H 190 TYR cc_start: 0.8230 (m-80) cc_final: 0.7805 (m-80) REVERT: H 274 MET cc_start: 0.7344 (mmm) cc_final: 0.7009 (mmm) outliers start: 16 outliers final: 12 residues processed: 137 average time/residue: 0.0898 time to fit residues: 19.0706 Evaluate side-chains 124 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 821 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 1 optimal weight: 9.9990 chunk 73 optimal weight: 0.0870 chunk 118 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.080599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.060634 restraints weight = 48602.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.062154 restraints weight = 26274.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.063129 restraints weight = 18009.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063733 restraints weight = 14201.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.064107 restraints weight = 12297.328| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12530 Z= 0.175 Angle : 0.654 8.732 17704 Z= 0.376 Chirality : 0.042 0.301 1988 Planarity : 0.004 0.049 1651 Dihedral : 28.018 175.179 3232 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.86 % Allowed : 14.50 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.25), residues: 1039 helix: 1.09 (0.24), residues: 463 sheet: -0.78 (0.36), residues: 196 loop : -0.54 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 35 TYR 0.027 0.002 TYR G 52 PHE 0.017 0.002 PHE C 13 TRP 0.005 0.001 TRP H 224 HIS 0.005 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.18 (12530) covalent geometry : angle 0.65369 / 0.38 (17704) hydrogen bonds : bond 0.04208 / 4.40 ( 593) hydrogen bonds : angle 4.56980 / 5.71 ( 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 127 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8036 (m-30) cc_final: 0.7644 (t70) REVERT: F 46 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8759 (tppp) REVERT: F 77 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7249 (tm-30) REVERT: G 31 ASN cc_start: 0.8215 (m-40) cc_final: 0.7776 (m-40) REVERT: H 1 MET cc_start: 0.7065 (tpt) cc_final: 0.6785 (tpt) REVERT: H 2 MET cc_start: 0.7491 (ttt) cc_final: 0.6986 (ttp) REVERT: H 95 MET cc_start: 0.6444 (mmt) cc_final: 0.5777 (mtt) REVERT: H 190 TYR cc_start: 0.8324 (m-80) cc_final: 0.7828 (m-80) REVERT: H 274 MET cc_start: 0.7445 (mmm) cc_final: 0.7190 (mmm) REVERT: H 278 MET cc_start: 0.8065 (mmm) cc_final: 0.7767 (mmp) outliers start: 16 outliers final: 15 residues processed: 122 average time/residue: 0.0836 time to fit residues: 16.3235 Evaluate side-chains 121 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 30 SER 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 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 158 THR 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 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: 6.9990 chunk 113 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.080359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060433 restraints weight = 48580.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061953 restraints weight = 26345.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062917 restraints weight = 18025.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063466 restraints weight = 14232.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.063893 restraints weight = 12388.752| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12530 Z= 0.172 Angle : 0.639 9.216 17704 Z= 0.367 Chirality : 0.042 0.303 1988 Planarity : 0.004 0.044 1651 Dihedral : 27.975 175.383 3232 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.90 % Allowed : 13.69 % Favored : 83.41 % 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: 0.25 (0.26), residues: 1039 helix: 1.16 (0.24), residues: 461 sheet: -0.67 (0.34), residues: 213 loop : -0.44 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 810 TYR 0.028 0.002 TYR G 52 PHE 0.019 0.002 PHE C 13 TRP 0.010 0.001 TRP H 638 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (12530) covalent geometry : angle 0.63886 / 0.37 (17704) hydrogen bonds : bond 0.04057 / 4.25 ( 593) hydrogen bonds : angle 4.50227 / 5.63 ( 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 137 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8037 (m-30) cc_final: 0.7675 (t70) REVERT: F 39 PHE cc_start: 0.8956 (t80) cc_final: 0.8579 (t80) REVERT: F 46 LYS cc_start: 0.9125 (ttpp) cc_final: 0.8760 (tppp) REVERT: G 31 ASN cc_start: 0.8231 (m-40) cc_final: 0.7834 (m-40) REVERT: H 1 MET cc_start: 0.7126 (tpt) cc_final: 0.6817 (tpt) REVERT: H 2 MET cc_start: 0.7579 (ttt) cc_final: 0.6922 (tmm) REVERT: H 4 ILE cc_start: 0.8198 (mp) cc_final: 0.7914 (mp) REVERT: H 95 MET cc_start: 0.6177 (mmt) cc_final: 0.5576 (mtt) REVERT: H 190 TYR cc_start: 0.8269 (m-80) cc_final: 0.7780 (m-80) REVERT: H 274 MET cc_start: 0.7378 (mmm) cc_final: 0.7141 (mmm) REVERT: H 278 MET cc_start: 0.8149 (mmm) cc_final: 0.7873 (mmt) outliers start: 25 outliers final: 20 residues processed: 129 average time/residue: 0.0831 time to fit residues: 17.2209 Evaluate side-chains 123 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 30 SER 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 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 55 LEU 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 747 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: 10.0000 chunk 54 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.082047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.064754 restraints weight = 49216.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.064029 restraints weight = 33940.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064565 restraints weight = 25871.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.064894 restraints weight = 20817.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.064970 restraints weight = 18647.609| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3252 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 : 0.626 7.415 17704 Z= 0.361 Chirality : 0.041 0.305 1988 Planarity : 0.004 0.042 1651 Dihedral : 27.849 175.566 3232 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.20 % Allowed : 14.27 % Favored : 83.53 % 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: 1.25 (0.24), residues: 461 sheet: -0.72 (0.34), residues: 215 loop : -0.42 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 810 TYR 0.033 0.001 TYR G 52 PHE 0.017 0.001 PHE C 13 TRP 0.010 0.001 TRP H 33 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (12530) covalent geometry : angle 0.62583 / 0.36 (17704) hydrogen bonds : bond 0.03894 / 4.08 ( 593) hydrogen bonds : angle 4.42722 / 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 126 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8044 (m-30) cc_final: 0.7688 (t70) REVERT: F 46 LYS cc_start: 0.9036 (ttpp) cc_final: 0.8764 (tppp) REVERT: G 31 ASN cc_start: 0.8145 (m-40) cc_final: 0.7774 (m-40) REVERT: H 1 MET cc_start: 0.7299 (tpt) cc_final: 0.7013 (tpt) REVERT: H 2 MET cc_start: 0.7621 (ttt) cc_final: 0.7221 (tmm) REVERT: H 95 MET cc_start: 0.6145 (mmt) cc_final: 0.5529 (mtp) REVERT: H 190 TYR cc_start: 0.8040 (m-80) cc_final: 0.7680 (m-80) REVERT: H 278 MET cc_start: 0.8115 (mmm) cc_final: 0.7798 (mmt) outliers start: 19 outliers final: 17 residues processed: 120 average time/residue: 0.0910 time to fit residues: 17.2720 Evaluate side-chains 117 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain D residue 50 SER 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 30 SER Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain H residue 7 VAL 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: 9.9990 chunk 83 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 HIS H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.078231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.058292 restraints weight = 49025.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.059678 restraints weight = 27678.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.060502 restraints weight = 19449.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.061135 restraints weight = 15692.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061464 restraints weight = 13660.789| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12530 Z= 0.271 Angle : 0.746 8.691 17704 Z= 0.416 Chirality : 0.046 0.301 1988 Planarity : 0.005 0.049 1651 Dihedral : 28.072 175.173 3232 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.90 % Allowed : 14.04 % Favored : 83.06 % 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: -0.23 (0.26), residues: 1039 helix: 0.91 (0.24), residues: 462 sheet: -1.33 (0.35), residues: 202 loop : -0.62 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 63 TYR 0.034 0.003 TYR G 52 PHE 0.031 0.003 PHE C 13 TRP 0.010 0.002 TRP E 91 HIS 0.006 0.001 HIS F 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.27 (12530) covalent geometry : angle 0.74611 / 0.42 (17704) hydrogen bonds : bond 0.05204 / 5.47 ( 593) hydrogen bonds : angle 4.75493 / 5.97 ( 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 127 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7711 (t0) cc_final: 0.7390 (t0) REVERT: D 68 ASP cc_start: 0.8124 (m-30) cc_final: 0.7714 (t70) REVERT: F 46 LYS cc_start: 0.9149 (ttpp) cc_final: 0.8805 (tppp) REVERT: G 31 ASN cc_start: 0.8228 (m-40) cc_final: 0.7840 (m-40) REVERT: H 1 MET cc_start: 0.7133 (tpt) cc_final: 0.6702 (tpt) REVERT: H 190 TYR cc_start: 0.8246 (m-80) cc_final: 0.7770 (m-80) outliers start: 25 outliers final: 20 residues processed: 121 average time/residue: 0.0894 time to fit residues: 17.0174 Evaluate side-chains 118 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 62 TYR 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 30 SER Chi-restraints excluded: chain H residue 4 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.079821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059991 restraints weight = 48218.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061487 restraints weight = 26294.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.062448 restraints weight = 18077.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.063044 restraints weight = 14280.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063389 restraints weight = 12371.242| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12530 Z= 0.158 Angle : 0.639 8.474 17704 Z= 0.367 Chirality : 0.042 0.316 1988 Planarity : 0.004 0.038 1651 Dihedral : 27.859 176.590 3232 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.32 % Allowed : 15.31 % 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: 0.08 (0.26), residues: 1039 helix: 1.17 (0.24), residues: 465 sheet: -0.99 (0.34), residues: 218 loop : -0.60 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.033 0.002 TYR G 52 PHE 0.016 0.001 PHE C 13 TRP 0.006 0.001 TRP H 638 HIS 0.004 0.001 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (12530) covalent geometry : angle 0.63925 / 0.37 (17704) hydrogen bonds : bond 0.03852 / 4.04 ( 593) hydrogen bonds : angle 4.46164 / 5.65 ( 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 127 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8067 (m-30) cc_final: 0.7670 (t70) REVERT: F 39 PHE cc_start: 0.8899 (t80) cc_final: 0.8621 (t80) REVERT: F 46 LYS cc_start: 0.9136 (ttpp) cc_final: 0.8831 (tppp) REVERT: G 31 ASN cc_start: 0.8248 (m-40) cc_final: 0.7863 (m-40) REVERT: H 1 MET cc_start: 0.7282 (tpt) cc_final: 0.6952 (tpt) REVERT: H 2 MET cc_start: 0.7506 (ttp) cc_final: 0.6653 (tmm) REVERT: H 190 TYR cc_start: 0.8158 (m-80) cc_final: 0.7800 (m-80) outliers start: 20 outliers final: 16 residues processed: 119 average time/residue: 0.0863 time to fit residues: 16.2256 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 : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 SER 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 114 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 29 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 100 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 80 GLN ** 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 = 0.3756 r_free = 0.3756 target = 0.079682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.059911 restraints weight = 48037.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061405 restraints weight = 26177.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.062341 restraints weight = 17984.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.062943 restraints weight = 14280.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.063272 restraints weight = 12389.613| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12530 Z= 0.167 Angle : 0.652 8.327 17704 Z= 0.371 Chirality : 0.042 0.300 1988 Planarity : 0.004 0.037 1651 Dihedral : 27.885 177.741 3232 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.20 % Allowed : 15.55 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.26), residues: 1039 helix: 1.23 (0.24), residues: 465 sheet: -0.92 (0.35), residues: 216 loop : -0.67 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 63 TYR 0.035 0.002 TYR G 52 PHE 0.018 0.002 PHE C 13 TRP 0.007 0.001 TRP F 91 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (12530) covalent geometry : angle 0.65167 / 0.37 (17704) hydrogen bonds : bond 0.03985 / 4.14 ( 593) hydrogen bonds : angle 4.46193 / 5.63 ( 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: 19 poor density : 103 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7637 (t0) cc_final: 0.7378 (t0) REVERT: D 68 ASP cc_start: 0.8094 (m-30) cc_final: 0.7677 (t70) REVERT: E 95 ASP cc_start: 0.7881 (m-30) cc_final: 0.7204 (m-30) REVERT: F 39 PHE cc_start: 0.8926 (t80) cc_final: 0.8650 (t80) REVERT: F 46 LYS cc_start: 0.9134 (ttpp) cc_final: 0.8793 (tppp) REVERT: G 31 ASN cc_start: 0.8260 (m-40) cc_final: 0.7886 (m-40) REVERT: H 1 MET cc_start: 0.7229 (tpt) cc_final: 0.6908 (tpt) REVERT: H 2 MET cc_start: 0.7549 (ttp) cc_final: 0.6864 (tmm) REVERT: H 190 TYR cc_start: 0.8197 (m-80) cc_final: 0.7836 (m-80) outliers start: 19 outliers final: 18 residues processed: 113 average time/residue: 0.0888 time to fit residues: 15.6259 Evaluate side-chains 119 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 50 SER 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 13 MET 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 29 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 52 optimal weight: 7.9990 chunk 70 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3820 r_free = 0.3820 target = 0.082050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.063515 restraints weight = 48868.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.064174 restraints weight = 30248.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.064632 restraints weight = 20490.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.064961 restraints weight = 19227.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.064938 restraints weight = 16649.918| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12530 Z= 0.146 Angle : 0.623 9.095 17704 Z= 0.359 Chirality : 0.041 0.321 1988 Planarity : 0.004 0.039 1651 Dihedral : 27.810 176.012 3232 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.20 % Allowed : 15.31 % 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: 0.24 (0.26), residues: 1039 helix: 1.33 (0.24), residues: 465 sheet: -0.85 (0.34), residues: 216 loop : -0.62 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 63 TYR 0.029 0.001 TYR G 52 PHE 0.014 0.001 PHE C 13 TRP 0.007 0.001 TRP H 638 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (12530) covalent geometry : angle 0.62337 / 0.36 (17704) hydrogen bonds : bond 0.03731 / 3.89 ( 593) hydrogen bonds : angle 4.33081 / 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 122 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7644 (t0) cc_final: 0.7416 (m-40) REVERT: D 68 ASP cc_start: 0.8065 (m-30) cc_final: 0.7690 (t70) REVERT: E 95 ASP cc_start: 0.7935 (m-30) cc_final: 0.7303 (m-30) REVERT: F 46 LYS cc_start: 0.9048 (ttpp) cc_final: 0.8744 (tppp) REVERT: G 31 ASN cc_start: 0.8219 (m-40) cc_final: 0.7820 (m-40) REVERT: H 1 MET cc_start: 0.7389 (tpt) cc_final: 0.7098 (tpt) REVERT: H 190 TYR cc_start: 0.8041 (m-80) cc_final: 0.7771 (m-80) outliers start: 19 outliers final: 18 residues processed: 113 average time/residue: 0.0909 time to fit residues: 15.8442 Evaluate side-chains 119 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 50 SER 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 114 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 29 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 73 optimal weight: 0.3980 chunk 113 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 80 GLN ** 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 = 0.3817 r_free = 0.3817 target = 0.081920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.063405 restraints weight = 48987.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.064136 restraints weight = 30230.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.064428 restraints weight = 20407.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.065202 restraints weight = 19083.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065146 restraints weight = 16003.086| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12530 Z= 0.152 Angle : 0.633 8.465 17704 Z= 0.362 Chirality : 0.041 0.309 1988 Planarity : 0.004 0.037 1651 Dihedral : 27.813 176.415 3232 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.20 % Allowed : 15.78 % Favored : 82.02 % 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: 0.25 (0.26), residues: 1039 helix: 1.39 (0.24), residues: 465 sheet: -0.86 (0.34), residues: 218 loop : -0.67 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 668 TYR 0.035 0.001 TYR G 52 PHE 0.049 0.002 PHE F 39 TRP 0.007 0.001 TRP H 638 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (12530) covalent geometry : angle 0.63340 / 0.36 (17704) hydrogen bonds : bond 0.03804 / 3.95 ( 593) hydrogen bonds : angle 4.34065 / 5.47 ( 1561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.78 seconds wall clock time: 40 minutes 32.96 seconds (2432.96 seconds total)