Starting phenix.real_space_refine on Fri Jul 3 18:32:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2q_53537/07_2026/9r2q_53537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2q_53537/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9r2q_53537/07_2026/9r2q_53537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2q_53537/07_2026/9r2q_53537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r2q_53537/07_2026/9r2q_53537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2q_53537/07_2026/9r2q_53537.map" } 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-dev-6108/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: 3.49, per 1000 atoms: 0.22 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: 1.17 Conformation dependent library (CDL) restraints added in 651.2 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: 2.44 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: 3.35 Time building geometry restraints manager: 1.63 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: 21463 1.69 - 3.38: 1946 3.38 - 5.07: 490 5.07 - 6.77: 76 6.77 - 8.46: 3 Bond angle restraints: 23978 Sorted by residual: 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=" O3' DT J 58 " pdb=" P DA J 59 " pdb=" O5' DA J 59 " ideal model delta sigma weight residual 104.00 96.69 7.31 1.50e+00 4.44e-01 2.37e+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=" 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 angle pdb=" O5' DG J 138 " pdb=" C5' DG J 138 " pdb=" C4' DG J 138 " ideal model delta sigma weight residual 109.40 113.06 -3.66 8.00e-01 1.56e+00 2.09e+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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.440 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- 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= 0.758 Angle : 1.093 8.457 23978 Z= 0.733 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 1.09291 / 0.73 (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 : 0.457 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: 0.1674 time to fit residues: 64.8242 Evaluate side-chains 214 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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: 9.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 69 GLN B 26 ASN D 64 ASN D 68 ASN E 94 GLN F 26 ASN G 113 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.140028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.093035 restraints weight = 37117.079| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.44 r_work: 0.3146 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16699 Z= 0.211 Angle : 0.801 8.839 23978 Z= 0.426 Chirality : 0.046 0.178 2816 Planarity : 0.006 0.054 2173 Dihedral : 29.497 79.267 4750 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.77 % Allowed : 10.20 % Favored : 87.03 % 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: 1.59 (0.21), residues: 1528 helix: 1.57 (0.20), residues: 613 sheet: 0.98 (0.29), residues: 324 loop : 0.73 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 33 TYR 0.015 0.002 TYR A 42 PHE 0.011 0.002 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.009 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (16699) covalent geometry : angle 0.80091 / 0.43 (23978) hydrogen bonds : bond 0.05944 / 4.07 ( 977) hydrogen bonds : angle 4.06962 / 2.95 ( 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 260 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8990 (tt0) cc_final: 0.8779 (tt0) REVERT: C 40 TYR cc_start: 0.8693 (m-80) cc_final: 0.8475 (m-80) REVERT: D 86 LYS cc_start: 0.9272 (mtmm) cc_final: 0.9068 (mttp) REVERT: E 40 HIS cc_start: 0.8114 (t70) cc_final: 0.7629 (t-90) REVERT: E 121 MET cc_start: 0.8101 (mtp) cc_final: 0.7778 (mtt) REVERT: G 14 LYS cc_start: 0.9246 (tptp) cc_final: 0.9035 (tppt) outliers start: 19 outliers final: 12 residues processed: 251 average time/residue: 0.1433 time to fit residues: 50.3128 Evaluate side-chains 227 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 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 92 SER 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: 9.9990 chunk 177 optimal weight: 40.0000 chunk 158 optimal weight: 10.0000 chunk 168 optimal weight: 50.0000 chunk 125 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 140 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 175 optimal weight: 20.0000 overall best weight: 4.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN D 64 ASN D 96 GLN G 105 GLN H 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.135032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088091 restraints weight = 36954.188| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.30 r_work: 0.3064 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 16699 Z= 0.322 Angle : 0.791 13.619 23978 Z= 0.427 Chirality : 0.050 0.277 2816 Planarity : 0.006 0.053 2173 Dihedral : 29.065 69.536 4750 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.37 % Allowed : 10.35 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.21), residues: 1528 helix: 1.80 (0.20), residues: 613 sheet: 0.93 (0.30), residues: 304 loop : 0.80 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 18 TYR 0.027 0.002 TYR F 89 PHE 0.018 0.002 PHE E 68 TRP 0.000 0.000 TRP K 146 HIS 0.009 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.32 (16699) covalent geometry : angle 0.79077 / 0.43 (23978) hydrogen bonds : bond 0.06471 / 4.42 ( 977) hydrogen bonds : angle 3.88278 / 2.81 ( 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 265 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8950 (tt0) cc_final: 0.8659 (tt0) REVERT: B 92 LYS cc_start: 0.9146 (tttt) cc_final: 0.8822 (ttpt) REVERT: C 77 THR cc_start: 0.8671 (p) cc_final: 0.8386 (t) REVERT: C 78 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8311 (ttm170) REVERT: D 80 ARG cc_start: 0.8988 (mtm-85) cc_final: 0.8771 (mtm110) REVERT: E 40 HIS cc_start: 0.8251 (t70) cc_final: 0.7877 (t-90) REVERT: E 54 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8263 (ttm170) REVERT: H 89 THR cc_start: 0.9396 (m) cc_final: 0.9173 (t) outliers start: 30 outliers final: 15 residues processed: 254 average time/residue: 0.1534 time to fit residues: 53.7447 Evaluate side-chains 227 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 78 ARG Chi-restraints excluded: chain D residue 39 SER 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 54 ARG Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 46 ARG Chi-restraints excluded: chain F residue 83 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 111 optimal weight: 30.0000 chunk 110 optimal weight: 0.0470 chunk 41 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN B 76 HIS D 64 ASN F 26 ASN H 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.137864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.091352 restraints weight = 36715.131| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.27 r_work: 0.3135 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16699 Z= 0.129 Angle : 0.630 10.712 23978 Z= 0.353 Chirality : 0.043 0.215 2816 Planarity : 0.004 0.046 2173 Dihedral : 28.687 71.543 4750 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.62 % Allowed : 14.14 % Favored : 83.24 % 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: 2.29 (0.21), residues: 1528 helix: 2.40 (0.20), residues: 615 sheet: 1.00 (0.30), residues: 304 loop : 1.03 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 73 TYR 0.025 0.001 TYR F 89 PHE 0.019 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.13 (16699) covalent geometry : angle 0.63004 / 0.35 (23978) hydrogen bonds : bond 0.04604 / 3.14 ( 977) hydrogen bonds : angle 3.40477 / 2.46 ( 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 248 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8125 (tp30) cc_final: 0.7832 (tp30) REVERT: B 92 LYS cc_start: 0.9036 (tttt) cc_final: 0.8739 (ttpt) REVERT: C 77 THR cc_start: 0.8575 (p) cc_final: 0.8325 (t) REVERT: C 100 ARG cc_start: 0.8898 (mmm160) cc_final: 0.8542 (mmt-90) REVERT: D 36 GLU cc_start: 0.5698 (tp30) cc_final: 0.5462 (tm-30) REVERT: D 93 ARG cc_start: 0.8982 (mtp85) cc_final: 0.8583 (ttp80) REVERT: E 40 HIS cc_start: 0.8253 (t70) cc_final: 0.7873 (t-90) REVERT: E 43 ARG cc_start: 0.8485 (mtm110) cc_final: 0.8173 (ptm-80) REVERT: E 121 MET cc_start: 0.8164 (mtp) cc_final: 0.7955 (mtt) REVERT: H 69 ASP cc_start: 0.8965 (t0) cc_final: 0.8686 (t0) REVERT: H 85 ASN cc_start: 0.9061 (m-40) cc_final: 0.8738 (m-40) REVERT: H 89 THR cc_start: 0.9359 (m) cc_final: 0.9140 (t) outliers start: 18 outliers final: 8 residues processed: 239 average time/residue: 0.1387 time to fit residues: 45.9256 Evaluate side-chains 233 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 225 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 46 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 9.9990 chunk 105 optimal weight: 40.0000 chunk 106 optimal weight: 20.0000 chunk 151 optimal weight: 40.0000 chunk 139 optimal weight: 50.0000 chunk 173 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 114 optimal weight: 7.9990 chunk 100 optimal weight: 0.0170 chunk 25 optimal weight: 6.9990 overall best weight: 3.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 64 ASN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.135116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.087496 restraints weight = 36934.167| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.24 r_work: 0.3072 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16699 Z= 0.222 Angle : 0.667 14.289 23978 Z= 0.365 Chirality : 0.045 0.236 2816 Planarity : 0.005 0.057 2173 Dihedral : 28.711 70.615 4750 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.77 % Allowed : 13.99 % Favored : 83.24 % 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: 2.31 (0.21), residues: 1528 helix: 2.45 (0.20), residues: 615 sheet: 0.99 (0.30), residues: 304 loop : 1.02 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 30 TYR 0.023 0.002 TYR F 89 PHE 0.011 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 0.00460 / 0.22 (16699) covalent geometry : angle 0.66704 / 0.36 (23978) hydrogen bonds : bond 0.05186 / 3.55 ( 977) hydrogen bonds : angle 3.44814 / 2.49 ( 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 244 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: B 64 GLU cc_start: 0.8830 (tt0) cc_final: 0.8628 (mt-10) REVERT: B 92 LYS cc_start: 0.9096 (tttt) cc_final: 0.8767 (ttpt) REVERT: C 77 THR cc_start: 0.8702 (p) cc_final: 0.8399 (t) REVERT: C 100 ARG cc_start: 0.8932 (mmm160) cc_final: 0.8570 (mmt-90) REVERT: C 119 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8526 (mmmm) REVERT: D 36 GLU cc_start: 0.5901 (tp30) cc_final: 0.5509 (tp30) REVERT: D 93 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8657 (mtp85) REVERT: E 40 HIS cc_start: 0.8334 (t70) cc_final: 0.7996 (t-90) REVERT: E 82 ASP cc_start: 0.8991 (t0) cc_final: 0.8592 (t70) REVERT: H 85 ASN cc_start: 0.9100 (m-40) cc_final: 0.8772 (m-40) REVERT: H 89 THR cc_start: 0.9410 (m) cc_final: 0.9186 (t) outliers start: 19 outliers final: 14 residues processed: 238 average time/residue: 0.1410 time to fit residues: 46.0961 Evaluate side-chains 233 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 CYS 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 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 81 THR Chi-restraints excluded: chain F residue 46 ARG 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: 0.3980 chunk 67 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 100 optimal weight: 50.0000 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 170 optimal weight: 20.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.136558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089810 restraints weight = 36707.793| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.24 r_work: 0.3107 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16699 Z= 0.139 Angle : 0.600 15.320 23978 Z= 0.338 Chirality : 0.042 0.199 2816 Planarity : 0.004 0.038 2173 Dihedral : 28.427 72.373 4750 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.04 % Allowed : 14.72 % Favored : 83.24 % 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: 2.57 (0.21), residues: 1528 helix: 2.74 (0.20), residues: 617 sheet: 1.03 (0.30), residues: 304 loop : 1.12 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 100 TYR 0.026 0.001 TYR F 89 PHE 0.011 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.002 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (16699) covalent geometry : angle 0.60041 / 0.34 (23978) hydrogen bonds : bond 0.04257 / 2.93 ( 977) hydrogen bonds : angle 3.23376 / 2.33 ( 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 247 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8492 (ptp-110) cc_final: 0.7953 (mtm-85) REVERT: A 106 GLU cc_start: 0.8154 (tp30) cc_final: 0.7885 (tp30) REVERT: B 85 MET cc_start: 0.9111 (mmm) cc_final: 0.8704 (mmm) REVERT: B 89 TYR cc_start: 0.9305 (m-80) cc_final: 0.9045 (m-80) REVERT: B 92 LYS cc_start: 0.9103 (tttt) cc_final: 0.8788 (ttpt) REVERT: C 77 THR cc_start: 0.8663 (p) cc_final: 0.8393 (t) REVERT: C 100 ARG cc_start: 0.8856 (mmm160) cc_final: 0.8503 (mmt-90) REVERT: D 93 ARG cc_start: 0.8968 (mtp85) cc_final: 0.8764 (mtp85) REVERT: E 40 HIS cc_start: 0.8324 (t70) cc_final: 0.7992 (t-90) REVERT: E 82 ASP cc_start: 0.9001 (t0) cc_final: 0.8610 (t70) REVERT: H 85 ASN cc_start: 0.9041 (m-40) cc_final: 0.8706 (m-40) REVERT: H 89 THR cc_start: 0.9411 (m) cc_final: 0.9172 (t) REVERT: H 94 GLU cc_start: 0.9059 (mp0) cc_final: 0.8781 (mp0) outliers start: 14 outliers final: 10 residues processed: 239 average time/residue: 0.1397 time to fit residues: 46.2535 Evaluate side-chains 237 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 227 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 D residue 57 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 57 GLU 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: 3.9990 chunk 57 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 122 optimal weight: 0.0050 chunk 156 optimal weight: 50.0000 chunk 43 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.136561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.089433 restraints weight = 36830.438| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.22 r_work: 0.3110 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16699 Z= 0.141 Angle : 0.600 15.296 23978 Z= 0.337 Chirality : 0.042 0.269 2816 Planarity : 0.004 0.039 2173 Dihedral : 28.310 71.921 4750 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.04 % Allowed : 14.58 % 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: 2.67 (0.21), residues: 1528 helix: 2.82 (0.20), residues: 621 sheet: 1.04 (0.30), residues: 312 loop : 1.18 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 100 TYR 0.016 0.001 TYR F 89 PHE 0.015 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (16699) covalent geometry : angle 0.59995 / 0.34 (23978) hydrogen bonds : bond 0.04200 / 2.89 ( 977) hydrogen bonds : angle 3.20076 / 2.31 ( 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 242 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8532 (ptp-110) cc_final: 0.7974 (mtm-85) REVERT: A 106 GLU cc_start: 0.8112 (tp30) cc_final: 0.7869 (tp30) REVERT: B 92 LYS cc_start: 0.9115 (tttt) cc_final: 0.8786 (ttpt) REVERT: C 77 THR cc_start: 0.8679 (p) cc_final: 0.8401 (t) REVERT: C 100 ARG cc_start: 0.8901 (mmm160) cc_final: 0.8554 (mmt-90) REVERT: D 93 ARG cc_start: 0.8971 (mtp85) cc_final: 0.8756 (mtp85) REVERT: E 40 HIS cc_start: 0.8352 (t70) cc_final: 0.8025 (t-90) REVERT: E 82 ASP cc_start: 0.9040 (t0) cc_final: 0.8651 (t70) REVERT: G 36 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7938 (ttp-110) REVERT: G 74 ASN cc_start: 0.8897 (m-40) cc_final: 0.8696 (t0) REVERT: H 85 ASN cc_start: 0.9053 (m-40) cc_final: 0.8710 (m-40) REVERT: H 89 THR cc_start: 0.9414 (m) cc_final: 0.9146 (t) REVERT: H 94 GLU cc_start: 0.9116 (mp0) cc_final: 0.8736 (mp0) outliers start: 14 outliers final: 9 residues processed: 234 average time/residue: 0.1340 time to fit residues: 43.5181 Evaluate side-chains 234 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 D residue 57 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain H residue 48 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 15 optimal weight: 0.9980 chunk 135 optimal weight: 30.0000 chunk 142 optimal weight: 50.0000 chunk 123 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 30.0000 chunk 166 optimal weight: 2.9990 chunk 102 optimal weight: 50.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 64 ASN D 96 GLN 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 = 0.135202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087747 restraints weight = 37068.659| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.22 r_work: 0.3081 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16699 Z= 0.189 Angle : 0.623 15.149 23978 Z= 0.345 Chirality : 0.043 0.189 2816 Planarity : 0.004 0.040 2173 Dihedral : 28.388 70.867 4750 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.48 % Allowed : 14.14 % 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: 2.79 (0.20), residues: 621 sheet: 1.11 (0.30), residues: 312 loop : 1.16 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 70 TYR 0.017 0.001 TYR B 89 PHE 0.018 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 0.00387 / 0.19 (16699) covalent geometry : angle 0.62267 / 0.35 (23978) hydrogen bonds : bond 0.04439 / 3.05 ( 977) hydrogen bonds : angle 3.22855 / 2.33 ( 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: 17 poor density : 221 time to evaluate : 0.461 Fit side-chains REVERT: A 43 ARG cc_start: 0.8641 (ptp-110) cc_final: 0.8073 (mtm-85) REVERT: A 69 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.9072 (tt0) REVERT: A 74 GLU cc_start: 0.8812 (tt0) cc_final: 0.8599 (tt0) REVERT: A 106 GLU cc_start: 0.8177 (tp30) cc_final: 0.7944 (tp30) REVERT: B 85 MET cc_start: 0.9137 (mmm) cc_final: 0.8775 (mmm) REVERT: B 92 LYS cc_start: 0.9157 (tttt) cc_final: 0.8828 (ttpt) REVERT: C 77 THR cc_start: 0.8739 (p) cc_final: 0.8455 (t) REVERT: C 100 ARG cc_start: 0.8865 (mmm160) cc_final: 0.8507 (mmt-90) REVERT: D 93 ARG cc_start: 0.8974 (mtp85) cc_final: 0.8736 (mtp85) REVERT: E 40 HIS cc_start: 0.8369 (t70) cc_final: 0.8046 (t-90) REVERT: E 82 ASP cc_start: 0.9002 (t0) cc_final: 0.8607 (t70) REVERT: G 36 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8012 (ttp-110) REVERT: G 74 ASN cc_start: 0.8927 (m-40) cc_final: 0.8715 (t0) REVERT: H 85 ASN cc_start: 0.9062 (m-40) cc_final: 0.8718 (m-40) REVERT: H 89 THR cc_start: 0.9420 (m) cc_final: 0.9154 (t) REVERT: H 94 GLU cc_start: 0.9150 (mp0) cc_final: 0.8738 (mp0) outliers start: 17 outliers final: 11 residues processed: 230 average time/residue: 0.1514 time to fit residues: 48.1350 Evaluate side-chains 231 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 77 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 104 optimal weight: 50.0000 chunk 95 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 175 optimal weight: 0.0040 chunk 102 optimal weight: 50.0000 chunk 157 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 150 optimal weight: 50.0000 overall best weight: 5.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN D 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.130363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.082757 restraints weight = 36382.904| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.23 r_work: 0.2975 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 16699 Z= 0.334 Angle : 0.814 17.004 23978 Z= 0.426 Chirality : 0.054 0.302 2816 Planarity : 0.006 0.057 2173 Dihedral : 29.271 76.415 4750 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.77 % Allowed : 14.72 % Favored : 82.51 % 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: 2.13 (0.21), residues: 1528 helix: 2.10 (0.20), residues: 626 sheet: 1.13 (0.31), residues: 284 loop : 1.00 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 30 TYR 0.023 0.002 TYR B 89 PHE 0.015 0.002 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.007 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.33 (16699) covalent geometry : angle 0.81394 / 0.43 (23978) hydrogen bonds : bond 0.06474 / 4.44 ( 977) hydrogen bonds : angle 3.70541 / 2.67 ( 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 232 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: B 85 MET cc_start: 0.9167 (mmm) cc_final: 0.8841 (mmm) REVERT: B 92 LYS cc_start: 0.9299 (tttt) cc_final: 0.8971 (ttpt) REVERT: C 78 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8219 (ttm170) REVERT: C 100 ARG cc_start: 0.8962 (mmm160) cc_final: 0.8619 (mmt-90) REVERT: D 52 ASP cc_start: 0.8734 (p0) cc_final: 0.8519 (p0) REVERT: D 93 ARG cc_start: 0.9020 (mtp85) cc_final: 0.8720 (mtp85) REVERT: E 40 HIS cc_start: 0.8339 (t70) cc_final: 0.8047 (t-90) REVERT: E 82 ASP cc_start: 0.8955 (t0) cc_final: 0.8559 (t70) REVERT: H 85 ASN cc_start: 0.9116 (m-40) cc_final: 0.8840 (m-40) outliers start: 19 outliers final: 15 residues processed: 226 average time/residue: 0.1546 time to fit residues: 47.9886 Evaluate side-chains 222 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 THR 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 41 SER Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 97 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 131 optimal weight: 50.0000 chunk 139 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN D 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.129094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.081387 restraints weight = 36441.338| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.26 r_work: 0.2960 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 16699 Z= 0.350 Angle : 0.811 16.358 23978 Z= 0.427 Chirality : 0.053 0.387 2816 Planarity : 0.006 0.073 2173 Dihedral : 29.418 80.590 4750 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.21 % Allowed : 14.43 % Favored : 82.36 % 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: 1.95 (0.21), residues: 1528 helix: 2.09 (0.20), residues: 626 sheet: 0.86 (0.31), residues: 280 loop : 0.84 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 24 TYR 0.017 0.002 TYR D 41 PHE 0.013 0.002 PHE F 101 TRP 0.000 0.000 TRP K 146 HIS 0.005 0.002 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.35 (16699) covalent geometry : angle 0.81051 / 0.43 (23978) hydrogen bonds : bond 0.05415 / 3.70 ( 977) hydrogen bonds : angle 3.75045 / 2.71 ( 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 233 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.449 Fit side-chains REVERT: A 43 ARG cc_start: 0.8903 (ptp-110) cc_final: 0.8325 (mtm-85) REVERT: B 85 MET cc_start: 0.9153 (mmm) cc_final: 0.8801 (mmm) REVERT: B 92 LYS cc_start: 0.9285 (tttt) cc_final: 0.8958 (ttpt) REVERT: C 21 ARG cc_start: 0.9122 (tpp80) cc_final: 0.8857 (ttm-80) REVERT: C 77 THR cc_start: 0.8858 (p) cc_final: 0.8585 (t) REVERT: C 78 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8221 (ttm170) REVERT: C 100 ARG cc_start: 0.8942 (mmm160) cc_final: 0.8600 (mmt-90) REVERT: E 40 HIS cc_start: 0.8340 (t70) cc_final: 0.8080 (t-90) REVERT: E 82 ASP cc_start: 0.8958 (t0) cc_final: 0.8572 (t70) REVERT: E 121 MET cc_start: 0.8446 (mtp) cc_final: 0.8241 (mtp) REVERT: H 85 ASN cc_start: 0.9135 (m-40) cc_final: 0.8829 (m-40) REVERT: H 89 THR cc_start: 0.9431 (m) cc_final: 0.9212 (t) outliers start: 22 outliers final: 17 residues processed: 224 average time/residue: 0.1551 time to fit residues: 47.7634 Evaluate side-chains 225 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 69 GLN 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 41 SER Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER 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: 20.0000 chunk 62 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.129226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.081498 restraints weight = 36502.106| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.25 r_work: 0.2966 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 16699 Z= 0.313 Angle : 0.945 59.199 23978 Z= 0.520 Chirality : 0.057 1.296 2816 Planarity : 0.006 0.072 2173 Dihedral : 29.432 80.569 4750 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.77 % Allowed : 14.87 % Favored : 82.36 % 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: 1.94 (0.21), residues: 1528 helix: 2.08 (0.20), residues: 626 sheet: 0.84 (0.31), residues: 280 loop : 0.83 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 33 TYR 0.017 0.002 TYR D 41 PHE 0.013 0.002 PHE F 101 TRP 0.000 0.000 TRP K 146 HIS 0.006 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.31 (16699) covalent geometry : angle 0.94454 / 0.52 (23978) hydrogen bonds : bond 0.05291 / 3.62 ( 977) hydrogen bonds : angle 3.74818 / 2.70 ( 2456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5236.84 seconds wall clock time: 89 minutes 32.74 seconds (5372.74 seconds total)