Starting phenix.real_space_refine on Thu Aug 6 13:53:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2q_53537/08_2026/9r2q_53537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2q_53537/08_2026/9r2q_53537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r2q_53537/08_2026/9r2q_53537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2q_53537/08_2026/9r2q_53537.map" model { file = "/net/cci-nas-00/data/ceres_data/9r2q_53537/08_2026/9r2q_53537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2q_53537/08_2026/9r2q_53537.cif" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 283 5.49 5 S 14 5.16 5 C 8991 2.51 5 N 3012 2.21 5 O 3555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15855 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2891 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "J" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2928 Classifications: {'DNA': 142} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 141} Chain: "K" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "L" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "M" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "N" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Time building chain proxies: 3.64, per 1000 atoms: 0.23 Number of scatterers: 15855 At special positions: 0 Unit cell: (107.315, 116.61, 185.055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 283 15.00 O 3555 8.00 N 3012 7.00 C 8991 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: 1.27 Conformation dependent library (CDL) restraints added in 608.5 milliseconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 18 sheets defined 41.6% alpha, 15.1% beta 142 base pairs and 278 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 removed outlier: 4.514A pdb=" N ARG A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.493A pdb=" N GLU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.112A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 86 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 66 through 80 removed outlier: 4.238A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.554A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.881A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.080A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 removed outlier: 4.842A pdb=" N LYS H 47 " --> pdb=" O TYR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 removed outlier: 3.600A pdb=" N ARG H 100 " --> pdb=" O GLN H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.540A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'K' and resid 277 through 289 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'L' and resid 277 through 289 Processing helix chain 'M' and resid 104 through 108 removed outlier: 4.005A pdb=" N TYR M 107 " --> pdb=" O GLN M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 277 through 288 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'N' and resid 277 through 289 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.961A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.099A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.611A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.853A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 6.792A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127 removed outlier: 6.215A pdb=" N MET K 133 " --> pdb=" O ARG K 273 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU K 257 " --> pdb=" O LEU K 265 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG K 267 " --> pdb=" O ILE K 255 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE K 255 " --> pdb=" O ARG K 267 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER K 269 " --> pdb=" O THR K 253 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR K 253 " --> pdb=" O SER K 269 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU K 271 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE K 251 " --> pdb=" O GLU K 271 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA K 161 " --> pdb=" O HIS K 214 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N HIS K 214 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 110 through 113 Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 127 removed outlier: 3.903A pdb=" N ILE L 251 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA L 161 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS L 214 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 110 through 112 Processing sheet with id=AB7, first strand: chain 'M' and resid 124 through 127 removed outlier: 3.980A pdb=" N ILE M 251 " --> pdb=" O VAL M 272 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N HIS M 214 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 110 through 112 Processing sheet with id=AB9, first strand: chain 'N' and resid 124 through 127 removed outlier: 3.984A pdb=" N ILE N 251 " --> pdb=" O VAL N 272 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA N 161 " --> pdb=" O HIS N 214 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N HIS N 214 " --> pdb=" O ALA N 161 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 361 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 278 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 1.73 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: 2714 1.33 - 1.45: 5265 1.45 - 1.57: 8172 1.57 - 1.69: 524 1.69 - 1.82: 24 Bond restraints: 16699 Sorted by residual: bond pdb=" C5' DC I 80 " pdb=" C4' DC I 80 " ideal model delta sigma weight residual 1.512 1.473 0.039 7.00e-03 2.04e+04 3.11e+01 bond pdb=" C3' DG I 19 " pdb=" C2' DG I 19 " ideal model delta sigma weight residual 1.516 1.558 -0.042 8.00e-03 1.56e+04 2.80e+01 bond pdb=" C3' DA I 120 " pdb=" C2' DA I 120 " ideal model delta sigma weight residual 1.516 1.557 -0.041 8.00e-03 1.56e+04 2.61e+01 bond pdb=" C3' DA I 131 " pdb=" O3' DA I 131 " ideal model delta sigma weight residual 1.435 1.369 0.066 1.30e-02 5.92e+03 2.58e+01 bond pdb=" C3' DA I 90 " pdb=" O3' DA I 90 " ideal model delta sigma weight residual 1.435 1.371 0.064 1.30e-02 5.92e+03 2.43e+01 ... (remaining 16694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 21418 1.69 - 3.38: 1980 3.38 - 5.07: 496 5.07 - 6.77: 81 6.77 - 8.46: 3 Bond angle restraints: 23978 Sorted by residual: angle pdb=" C3' DA I 90 " pdb=" O3' DA I 90 " pdb=" P DA I 91 " ideal model delta sigma weight residual 119.70 125.68 -5.98 1.20e+00 6.94e-01 2.48e+01 angle pdb=" O4' DG J 134 " pdb=" C1' DG J 134 " pdb=" N9 DG J 134 " ideal model delta sigma weight residual 108.00 111.45 -3.45 7.00e-01 2.04e+00 2.42e+01 angle pdb=" O5' DG J 128 " pdb=" C5' DG J 128 " pdb=" C4' DG J 128 " ideal model delta sigma weight residual 109.40 113.24 -3.84 8.00e-01 1.56e+00 2.30e+01 angle pdb=" C3' DC I 119 " pdb=" O3' DC I 119 " pdb=" P DA I 120 " ideal model delta sigma weight residual 119.70 125.40 -5.70 1.20e+00 6.94e-01 2.26e+01 angle pdb=" CA TYR H 43 " pdb=" CB TYR H 43 " pdb=" CG TYR H 43 " ideal model delta sigma weight residual 113.90 122.36 -8.46 1.80e+00 3.09e-01 2.21e+01 ... (remaining 23973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 6961 17.28 - 34.56: 923 34.56 - 51.84: 1121 51.84 - 69.12: 307 69.12 - 86.40: 3 Dihedral angle restraints: 9315 sinusoidal: 4849 harmonic: 4466 Sorted by residual: dihedral pdb=" CA ARG E 43 " pdb=" C ARG E 43 " pdb=" N PRO E 44 " pdb=" CA PRO E 44 " ideal model delta harmonic sigma weight residual -180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ARG A 84 " pdb=" C ARG A 84 " pdb=" N PHE A 85 " pdb=" CA PHE A 85 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA TYR E 42 " pdb=" C TYR E 42 " pdb=" N ARG E 43 " pdb=" CA ARG E 43 " ideal model delta harmonic sigma weight residual 180.00 157.11 22.89 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 9312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1981 0.072 - 0.144: 653 0.144 - 0.215: 144 0.215 - 0.287: 36 0.287 - 0.359: 2 Chirality restraints: 2816 Sorted by residual: chirality pdb=" CA TYR H 43 " pdb=" N TYR H 43 " pdb=" C TYR H 43 " pdb=" CB TYR H 43 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ARG L 248 " pdb=" N ARG L 248 " pdb=" C ARG L 248 " pdb=" CB ARG L 248 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ARG K 248 " pdb=" N ARG K 248 " pdb=" C ARG K 248 " pdb=" CB ARG K 248 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2813 not shown) Planarity restraints: 2173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 28 " -0.050 2.00e-02 2.50e+03 2.25e-02 1.27e+01 pdb=" N1 DT J 28 " 0.040 2.00e-02 2.50e+03 pdb=" C2 DT J 28 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT J 28 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DT J 28 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT J 28 " -0.008 2.00e-02 2.50e+03 pdb=" O4 DT J 28 " -0.019 2.00e-02 2.50e+03 pdb=" C5 DT J 28 " 0.005 2.00e-02 2.50e+03 pdb=" C7 DT J 28 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT J 28 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 120 " 0.045 2.00e-02 2.50e+03 1.92e-02 1.01e+01 pdb=" N9 DA I 120 " -0.038 2.00e-02 2.50e+03 pdb=" C8 DA I 120 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 120 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 120 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 120 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA I 120 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DA I 120 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DA I 120 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DA I 120 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DA I 120 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 18 " -0.045 2.00e-02 2.50e+03 1.82e-02 9.97e+00 pdb=" N9 DG J 18 " 0.036 2.00e-02 2.50e+03 pdb=" C8 DG J 18 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DG J 18 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG J 18 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG J 18 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG J 18 " -0.018 2.00e-02 2.50e+03 pdb=" N1 DG J 18 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG J 18 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG J 18 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DG J 18 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG J 18 " 0.003 2.00e-02 2.50e+03 ... (remaining 2170 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3623 2.80 - 3.33: 13670 3.33 - 3.85: 28072 3.85 - 4.38: 33714 4.38 - 4.90: 47627 Nonbonded interactions: 126706 Sorted by model distance: nonbonded pdb=" OG SER C 19 " pdb=" O LEU C 24 " model vdw 2.281 3.040 nonbonded pdb=" N ARG C 18 " pdb=" OP1 DT I 31 " model vdw 2.311 3.120 nonbonded pdb=" N GLU F 53 " pdb=" OE1 GLU F 53 " model vdw 2.313 3.120 nonbonded pdb=" OG1 THR D 91 " pdb=" OE1 GLU D 94 " model vdw 2.355 3.040 nonbonded pdb=" O6 DG I 126 " pdb=" N6 DA J 21 " model vdw 2.373 3.120 ... (remaining 126701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 18 through 119) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.740 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.008 0.066 16699 Z= 0.759 Angle : 1.103 8.457 23978 Z= 0.741 Chirality : 0.075 0.359 2816 Planarity : 0.007 0.068 2173 Dihedral : 25.241 86.404 6419 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.44 % Allowed : 2.48 % Favored : 97.08 % Cbeta Deviations : 0.07 % 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: 0.19 (0.20), residues: 1528 helix: -0.37 (0.18), residues: 607 sheet: 1.19 (0.29), residues: 272 loop : 0.39 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 33 TYR 0.041 0.003 TYR H 43 PHE 0.026 0.003 PHE H 71 TRP 0.000 0.000 TRP K 146 HIS 0.010 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00842 / 0.76 (16699) covalent geometry : angle 1.10274 / 0.74 (23978) hydrogen bonds : bond 0.14570 / 9.61 ( 977) hydrogen bonds : angle 6.02213 / 4.43 ( 2456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7970 (tt0) cc_final: 0.7658 (tt0) REVERT: G 69 ASN cc_start: 0.8146 (m-40) cc_final: 0.7784 (m-40) outliers start: 3 outliers final: 0 residues processed: 286 average time/residue: 0.1561 time to fit residues: 60.8215 Evaluate side-chains 215 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.0970 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 69 GLN B 26 ASN C 85 GLN D 64 ASN D 68 ASN E 94 GLN F 26 ASN G 113 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.138542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090887 restraints weight = 37165.268| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.39 r_work: 0.3108 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16699 Z= 0.243 Angle : 0.835 10.071 23978 Z= 0.432 Chirality : 0.049 0.219 2816 Planarity : 0.006 0.055 2173 Dihedral : 29.508 77.067 4750 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.06 % Allowed : 10.64 % Favored : 86.30 % 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: 1.56 (0.21), residues: 1528 helix: 1.54 (0.20), residues: 613 sheet: 0.95 (0.29), residues: 324 loop : 0.74 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 80 TYR 0.014 0.002 TYR F 89 PHE 0.013 0.002 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.010 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.24 (16699) covalent geometry : angle 0.83536 / 0.43 (23978) hydrogen bonds : bond 0.06194 / 4.27 ( 977) hydrogen bonds : angle 4.06294 / 2.94 ( 2456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.9039 (tt0) cc_final: 0.8803 (tt0) REVERT: B 92 LYS cc_start: 0.8809 (tttt) cc_final: 0.8531 (ttpt) REVERT: D 36 GLU cc_start: 0.5869 (tp30) cc_final: 0.5645 (tp30) REVERT: D 80 ARG cc_start: 0.9013 (mtm-85) cc_final: 0.8725 (mtm110) REVERT: E 40 HIS cc_start: 0.8143 (t70) cc_final: 0.7687 (t-90) REVERT: E 121 MET cc_start: 0.8160 (mtp) cc_final: 0.7848 (mtt) REVERT: H 58 LYS cc_start: 0.9292 (mttt) cc_final: 0.9020 (mtpp) outliers start: 21 outliers final: 12 residues processed: 250 average time/residue: 0.1373 time to fit residues: 48.1279 Evaluate side-chains 226 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 48 GLN Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 89 optimal weight: 10.0000 chunk 177 optimal weight: 50.0000 chunk 158 optimal weight: 9.9990 chunk 168 optimal weight: 40.0000 chunk 125 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 40.0000 chunk 140 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 175 optimal weight: 0.1980 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 94 GLN D 64 ASN D 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.134411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.087293 restraints weight = 36863.218| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.22 r_work: 0.3050 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 16699 Z= 0.307 Angle : 0.802 13.998 23978 Z= 0.428 Chirality : 0.051 0.285 2816 Planarity : 0.006 0.062 2173 Dihedral : 28.871 67.660 4750 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.79 % Allowed : 10.79 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.21), residues: 1528 helix: 1.90 (0.20), residues: 612 sheet: 0.92 (0.29), residues: 304 loop : 0.84 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 132 TYR 0.036 0.003 TYR H 43 PHE 0.015 0.002 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.008 0.002 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.31 (16699) covalent geometry : angle 0.80214 / 0.43 (23978) hydrogen bonds : bond 0.06389 / 4.34 ( 977) hydrogen bonds : angle 3.83212 / 2.78 ( 2456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8952 (tt0) cc_final: 0.8672 (tt0) REVERT: B 26 ASN cc_start: 0.8844 (m110) cc_final: 0.8618 (m110) REVERT: B 92 LYS cc_start: 0.9153 (tttt) cc_final: 0.8838 (ttpt) REVERT: C 77 THR cc_start: 0.8746 (p) cc_final: 0.8441 (t) REVERT: C 78 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8298 (ttm170) REVERT: E 40 HIS cc_start: 0.8238 (t70) cc_final: 0.7881 (t-90) REVERT: E 54 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8266 (ttm170) REVERT: G 95 ASN cc_start: 0.9222 (t0) cc_final: 0.8988 (t0) REVERT: H 85 ASN cc_start: 0.9081 (m110) cc_final: 0.8801 (m-40) outliers start: 26 outliers final: 9 residues processed: 246 average time/residue: 0.1498 time to fit residues: 51.3704 Evaluate side-chains 232 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 221 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain H residue 48 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 111 optimal weight: 40.0000 chunk 110 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN B 76 HIS D 50 HIS D 64 ASN E 94 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.137164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.090699 restraints weight = 36716.558| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.21 r_work: 0.3127 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16699 Z= 0.130 Angle : 0.641 10.840 23978 Z= 0.353 Chirality : 0.043 0.197 2816 Planarity : 0.005 0.084 2173 Dihedral : 28.550 71.306 4750 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.04 % Allowed : 13.12 % Favored : 84.84 % 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: 2.27 (0.21), residues: 1528 helix: 2.36 (0.20), residues: 617 sheet: 0.96 (0.29), residues: 304 loop : 1.06 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 100 TYR 0.026 0.001 TYR F 89 PHE 0.013 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.012 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (16699) covalent geometry : angle 0.64080 / 0.35 (23978) hydrogen bonds : bond 0.04585 / 3.14 ( 977) hydrogen bonds : angle 3.35877 / 2.42 ( 2456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 241 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8913 (tt0) cc_final: 0.8640 (tt0) REVERT: B 26 ASN cc_start: 0.8935 (m110) cc_final: 0.8640 (m110) REVERT: B 92 LYS cc_start: 0.9064 (tttt) cc_final: 0.8770 (ttpt) REVERT: C 77 THR cc_start: 0.8617 (p) cc_final: 0.8366 (t) REVERT: C 100 ARG cc_start: 0.8863 (mmm160) cc_final: 0.8520 (mmt-90) REVERT: D 88 SER cc_start: 0.9135 (OUTLIER) cc_final: 0.8907 (p) REVERT: D 93 ARG cc_start: 0.8911 (mtp-110) cc_final: 0.8541 (mtp85) REVERT: E 40 HIS cc_start: 0.8283 (t70) cc_final: 0.7931 (t-90) REVERT: G 95 ASN cc_start: 0.9151 (t0) cc_final: 0.8940 (t0) REVERT: H 85 ASN cc_start: 0.9002 (m110) cc_final: 0.8720 (m-40) outliers start: 14 outliers final: 9 residues processed: 247 average time/residue: 0.1400 time to fit residues: 48.2872 Evaluate side-chains 241 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 231 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 48 GLN Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 139 optimal weight: 50.0000 chunk 173 optimal weight: 0.7980 chunk 15 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 100 optimal weight: 0.2980 chunk 25 optimal weight: 5.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN C 32 HIS D 50 HIS D 64 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN G 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.136257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.089527 restraints weight = 36546.797| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.20 r_work: 0.3104 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16699 Z= 0.161 Angle : 0.630 13.890 23978 Z= 0.347 Chirality : 0.043 0.200 2816 Planarity : 0.004 0.042 2173 Dihedral : 28.369 71.541 4750 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.92 % Allowed : 12.83 % Favored : 84.26 % 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: 2.45 (0.21), residues: 1528 helix: 2.59 (0.20), residues: 617 sheet: 1.01 (0.30), residues: 304 loop : 1.09 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 30 TYR 0.025 0.001 TYR F 89 PHE 0.012 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (16699) covalent geometry : angle 0.63023 / 0.35 (23978) hydrogen bonds : bond 0.04494 / 3.08 ( 977) hydrogen bonds : angle 3.29460 / 2.37 ( 2456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8124 (tp30) cc_final: 0.7859 (tp30) REVERT: B 64 GLU cc_start: 0.8789 (tt0) cc_final: 0.8570 (mt-10) REVERT: B 92 LYS cc_start: 0.9052 (tttt) cc_final: 0.8745 (ttpt) REVERT: C 77 THR cc_start: 0.8680 (p) cc_final: 0.8409 (t) REVERT: C 100 ARG cc_start: 0.8844 (mmm160) cc_final: 0.8494 (mmt-90) REVERT: D 36 GLU cc_start: 0.5802 (tm-30) cc_final: 0.5542 (tm-30) REVERT: E 40 HIS cc_start: 0.8315 (t70) cc_final: 0.7982 (t-90) REVERT: E 82 ASP cc_start: 0.8926 (t0) cc_final: 0.8548 (t70) REVERT: H 85 ASN cc_start: 0.9020 (m110) cc_final: 0.8742 (m-40) outliers start: 20 outliers final: 11 residues processed: 240 average time/residue: 0.1456 time to fit residues: 48.5861 Evaluate side-chains 236 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 225 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain H residue 48 GLN Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 126 optimal weight: 8.9990 chunk 100 optimal weight: 0.0270 chunk 71 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 175 optimal weight: 30.0000 chunk 116 optimal weight: 50.0000 chunk 48 optimal weight: 0.9980 chunk 170 optimal weight: 30.0000 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN D 50 HIS D 64 ASN D 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.137523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.091130 restraints weight = 36722.657| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.22 r_work: 0.3136 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16699 Z= 0.124 Angle : 0.595 14.479 23978 Z= 0.333 Chirality : 0.041 0.180 2816 Planarity : 0.004 0.037 2173 Dihedral : 28.118 71.717 4750 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.33 % Allowed : 14.29 % Favored : 83.38 % 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: 2.66 (0.21), residues: 1528 helix: 2.86 (0.20), residues: 617 sheet: 0.99 (0.30), residues: 312 loop : 1.16 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 100 TYR 0.024 0.001 TYR F 89 PHE 0.012 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.002 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (16699) covalent geometry : angle 0.59472 / 0.33 (23978) hydrogen bonds : bond 0.04036 / 2.77 ( 977) hydrogen bonds : angle 3.13189 / 2.25 ( 2456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8965 (tt0) cc_final: 0.8732 (tt0) REVERT: A 106 GLU cc_start: 0.8104 (tp30) cc_final: 0.7841 (tp30) REVERT: B 85 MET cc_start: 0.8822 (mmm) cc_final: 0.8358 (mmm) REVERT: B 89 TYR cc_start: 0.9261 (m-80) cc_final: 0.8886 (m-80) REVERT: B 92 LYS cc_start: 0.9053 (tttt) cc_final: 0.8767 (ttpt) REVERT: C 77 THR cc_start: 0.8653 (p) cc_final: 0.8398 (t) REVERT: C 100 ARG cc_start: 0.8872 (mmm160) cc_final: 0.8532 (mmt-90) REVERT: C 119 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8511 (mmmm) REVERT: D 36 GLU cc_start: 0.5703 (tm-30) cc_final: 0.5388 (tm-30) REVERT: E 40 HIS cc_start: 0.8332 (t70) cc_final: 0.8009 (t-90) REVERT: E 82 ASP cc_start: 0.8934 (t0) cc_final: 0.8555 (t70) REVERT: H 69 ASP cc_start: 0.8954 (t0) cc_final: 0.8694 (t0) REVERT: H 85 ASN cc_start: 0.9002 (m110) cc_final: 0.8719 (m-40) REVERT: H 94 GLU cc_start: 0.9044 (mp0) cc_final: 0.8751 (mp0) outliers start: 16 outliers final: 8 residues processed: 238 average time/residue: 0.1489 time to fit residues: 49.3572 Evaluate side-chains 236 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 228 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain H residue 48 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 156 optimal weight: 50.0000 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 118 optimal weight: 0.0670 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN C 85 GLN D 64 ASN D 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.136911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090417 restraints weight = 36447.491| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.18 r_work: 0.3128 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16699 Z= 0.141 Angle : 0.599 14.139 23978 Z= 0.334 Chirality : 0.042 0.238 2816 Planarity : 0.004 0.042 2173 Dihedral : 28.076 71.379 4750 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.19 % Allowed : 15.16 % Favored : 82.65 % 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: 2.76 (0.21), residues: 1528 helix: 2.92 (0.20), residues: 621 sheet: 1.09 (0.30), residues: 312 loop : 1.21 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.013 0.001 TYR F 89 PHE 0.013 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (16699) covalent geometry : angle 0.59892 / 0.33 (23978) hydrogen bonds : bond 0.04094 / 2.81 ( 977) hydrogen bonds : angle 3.13857 / 2.26 ( 2456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8096 (tp30) cc_final: 0.7892 (tp30) REVERT: B 85 MET cc_start: 0.8900 (mmm) cc_final: 0.8530 (mmm) REVERT: B 89 TYR cc_start: 0.9219 (m-80) cc_final: 0.8917 (m-80) REVERT: B 92 LYS cc_start: 0.9076 (tttt) cc_final: 0.8765 (ttpt) REVERT: C 77 THR cc_start: 0.8645 (p) cc_final: 0.8386 (t) REVERT: C 100 ARG cc_start: 0.8861 (mmm160) cc_final: 0.8523 (mmt-90) REVERT: D 36 GLU cc_start: 0.5729 (tm-30) cc_final: 0.5491 (tm-30) REVERT: E 40 HIS cc_start: 0.8334 (t70) cc_final: 0.8015 (t-90) REVERT: E 82 ASP cc_start: 0.8962 (t0) cc_final: 0.8601 (t70) REVERT: H 85 ASN cc_start: 0.9011 (m110) cc_final: 0.8718 (m-40) REVERT: H 94 GLU cc_start: 0.9086 (mp0) cc_final: 0.8767 (mp0) outliers start: 15 outliers final: 11 residues processed: 231 average time/residue: 0.1593 time to fit residues: 50.9574 Evaluate side-chains 234 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 223 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 48 GLN Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 15 optimal weight: 1.9990 chunk 135 optimal weight: 50.0000 chunk 142 optimal weight: 30.0000 chunk 123 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 102 optimal weight: 50.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 64 ASN D 96 GLN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.135249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.088387 restraints weight = 36642.490| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.18 r_work: 0.3083 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16699 Z= 0.195 Angle : 0.630 13.903 23978 Z= 0.346 Chirality : 0.043 0.192 2816 Planarity : 0.004 0.041 2173 Dihedral : 28.222 70.410 4750 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.62 % Allowed : 14.72 % Favored : 82.65 % 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: 2.72 (0.21), residues: 1528 helix: 2.84 (0.20), residues: 621 sheet: 1.12 (0.30), residues: 312 loop : 1.21 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 70 TYR 0.013 0.001 TYR D 41 PHE 0.012 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.20 (16699) covalent geometry : angle 0.63015 / 0.35 (23978) hydrogen bonds : bond 0.04420 / 3.03 ( 977) hydrogen bonds : angle 3.20350 / 2.30 ( 2456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.9056 (tt0) REVERT: B 92 LYS cc_start: 0.9132 (tttt) cc_final: 0.8817 (ttpt) REVERT: C 77 THR cc_start: 0.8734 (p) cc_final: 0.8457 (t) REVERT: C 100 ARG cc_start: 0.8888 (mmm160) cc_final: 0.8547 (mmt-90) REVERT: D 36 GLU cc_start: 0.5899 (tm-30) cc_final: 0.5609 (tm-30) REVERT: E 40 HIS cc_start: 0.8373 (t70) cc_final: 0.8069 (t-90) REVERT: E 82 ASP cc_start: 0.8962 (t0) cc_final: 0.8592 (t70) REVERT: H 85 ASN cc_start: 0.9027 (m110) cc_final: 0.8736 (m-40) outliers start: 18 outliers final: 12 residues processed: 228 average time/residue: 0.1445 time to fit residues: 45.7611 Evaluate side-chains 230 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain H residue 48 GLN Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 104 optimal weight: 50.0000 chunk 95 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 102 optimal weight: 50.0000 chunk 157 optimal weight: 30.0000 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 150 optimal weight: 50.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN D 64 ASN D 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.132195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.084247 restraints weight = 36799.834| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.20 r_work: 0.3016 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 16699 Z= 0.271 Angle : 0.733 16.051 23978 Z= 0.389 Chirality : 0.049 0.240 2816 Planarity : 0.005 0.070 2173 Dihedral : 28.710 73.521 4750 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.77 % Allowed : 14.58 % Favored : 82.65 % 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: 2.34 (0.21), residues: 1528 helix: 2.40 (0.20), residues: 627 sheet: 1.01 (0.30), residues: 312 loop : 1.09 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 100 TYR 0.015 0.002 TYR D 41 PHE 0.022 0.002 PHE F 101 TRP 0.000 0.000 TRP K 146 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.27 (16699) covalent geometry : angle 0.73349 / 0.39 (23978) hydrogen bonds : bond 0.05336 / 3.65 ( 977) hydrogen bonds : angle 3.44791 / 2.49 ( 2456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8826 (mmm) cc_final: 0.8484 (tmm) REVERT: B 92 LYS cc_start: 0.9237 (tttt) cc_final: 0.8912 (ttpt) REVERT: C 77 THR cc_start: 0.8846 (p) cc_final: 0.8560 (t) REVERT: C 100 ARG cc_start: 0.8904 (mmm160) cc_final: 0.8553 (mmt-90) REVERT: D 36 GLU cc_start: 0.6203 (tm-30) cc_final: 0.5883 (tm-30) REVERT: E 40 HIS cc_start: 0.8346 (t70) cc_final: 0.8065 (t-90) REVERT: E 82 ASP cc_start: 0.8918 (t0) cc_final: 0.8515 (t70) REVERT: H 85 ASN cc_start: 0.9071 (m110) cc_final: 0.8793 (m-40) outliers start: 19 outliers final: 16 residues processed: 227 average time/residue: 0.1596 time to fit residues: 50.0467 Evaluate side-chains 228 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain H residue 48 GLN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 131 optimal weight: 50.0000 chunk 139 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 90 optimal weight: 10.9990 chunk 92 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 4 optimal weight: 0.0370 chunk 93 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 overall best weight: 6.1868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN B 76 HIS D 50 HIS D 64 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.128405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.080687 restraints weight = 36465.154| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.15 r_work: 0.2951 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 16699 Z= 0.370 Angle : 0.878 17.125 23978 Z= 0.452 Chirality : 0.056 0.377 2816 Planarity : 0.007 0.103 2173 Dihedral : 29.444 76.948 4750 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.62 % Allowed : 13.99 % Favored : 83.38 % 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: 1.71 (0.21), residues: 1528 helix: 1.85 (0.20), residues: 627 sheet: 0.72 (0.31), residues: 284 loop : 0.76 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 24 TYR 0.026 0.002 TYR B 89 PHE 0.011 0.002 PHE E 85 TRP 0.000 0.000 TRP K 146 HIS 0.007 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.37 (16699) covalent geometry : angle 0.87824 / 0.45 (23978) hydrogen bonds : bond 0.06316 / 4.31 ( 977) hydrogen bonds : angle 3.88168 / 2.81 ( 2456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: B 92 LYS cc_start: 0.9304 (tttt) cc_final: 0.8998 (ttpt) REVERT: B 93 ARG cc_start: 0.9035 (ptm160) cc_final: 0.8686 (ptm160) REVERT: C 77 THR cc_start: 0.8934 (p) cc_final: 0.8663 (t) REVERT: C 100 ARG cc_start: 0.8932 (mmm160) cc_final: 0.8585 (mmt-90) REVERT: D 52 ASP cc_start: 0.8798 (p0) cc_final: 0.8546 (p0) REVERT: E 40 HIS cc_start: 0.8316 (t70) cc_final: 0.8068 (t-90) REVERT: E 82 ASP cc_start: 0.8917 (t0) cc_final: 0.8527 (t70) REVERT: H 85 ASN cc_start: 0.9037 (m-40) cc_final: 0.8792 (m-40) outliers start: 18 outliers final: 13 residues processed: 221 average time/residue: 0.1450 time to fit residues: 44.9647 Evaluate side-chains 222 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 48 GLN Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 164 optimal weight: 50.0000 chunk 62 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 146 optimal weight: 40.0000 chunk 52 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 50 HIS ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.128635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.080934 restraints weight = 36434.158| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.15 r_work: 0.2957 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.228 16699 Z= 0.321 Angle : 1.000 59.128 23978 Z= 0.540 Chirality : 0.059 1.222 2816 Planarity : 0.006 0.094 2173 Dihedral : 29.454 77.105 4750 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.48 % Allowed : 14.14 % Favored : 83.38 % Cbeta Deviations : 0.07 % 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: 1.68 (0.21), residues: 1528 helix: 1.82 (0.20), residues: 627 sheet: 0.70 (0.31), residues: 284 loop : 0.74 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 24 TYR 0.027 0.002 TYR B 89 PHE 0.010 0.002 PHE E 68 TRP 0.000 0.000 TRP K 146 HIS 0.007 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.32 (16699) covalent geometry : angle 0.99961 / 0.54 (23978) hydrogen bonds : bond 0.06200 / 4.23 ( 977) hydrogen bonds : angle 3.87464 / 2.80 ( 2456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5157.94 seconds wall clock time: 88 minutes 2.39 seconds (5282.39 seconds total)