Starting phenix.real_space_refine on Sat Sep 12 00:41:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y60_33630/09_2026/7y60_33630.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y60_33630/09_2026/7y60_33630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y60_33630/09_2026/7y60_33630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y60_33630/09_2026/7y60_33630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y60_33630/09_2026/7y60_33630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y60_33630/09_2026/7y60_33630.map" } resolution = 3.8 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1848 atoms to isotropic. 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 216 5.49 5 S 20 5.16 5 C 6418 2.51 5 N 2172 2.21 5 O 2552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11378 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 761 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "F" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 591 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2198 Classifications: {'DNA': 108} Link IDs: {'rna3p': 107} Chain: "C" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 732 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "D" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 583 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "J" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2230 Classifications: {'DNA': 108} Link IDs: {'rna3p': 107} Chain: "K" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 99 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "L" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 1749 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 13, 'TRANS': 340} Chain breaks: 4 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1113 Unresolved non-hydrogen angles: 1439 Unresolved non-hydrogen dihedrals: 949 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLU:plan': 14, 'TRP:plan': 8, 'HIS:plan': 10, 'ASN:plan1': 15, 'TYR:plan': 13, 'ASP:plan': 22, 'PHE:plan': 17, 'GLN:plan1': 7, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 600 Time building chain proxies: 2.60, per 1000 atoms: 0.23 Number of scatterers: 11378 At special positions: 0 Unit cell: (107, 116, 122, 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 20 16.00 P 216 15.00 O 2552 8.00 N 2172 7.00 C 6418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 356.6 milliseconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 49.4% alpha, 15.4% beta 97 base pairs and 169 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'G' and resid 63 through 79 Processing helix chain 'G' and resid 85 through 114 removed outlier: 3.786A pdb=" N ALA G 114 " --> pdb=" O CYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 132 removed outlier: 3.573A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 49 through 77 removed outlier: 4.122A pdb=" N ARG H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN H 64 " --> pdb=" O VAL H 60 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.820A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.325A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.735A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.787A pdb=" N SER C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 77 removed outlier: 3.736A pdb=" N ASP C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 removed outlier: 3.502A pdb=" N ILE C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.761A pdb=" N ARG D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.736A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.505A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 4.054A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.703A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.201A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 703 through 707 removed outlier: 3.643A pdb=" N GLN K 706 " --> pdb=" O VAL K 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.831A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.917A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'L' and resid 2 through 5 removed outlier: 6.881A pdb=" N PHE L 360 " --> pdb=" O TRP L 354 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP L 354 " --> pdb=" O PHE L 360 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA L 362 " --> pdb=" O ILE L 352 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE L 352 " --> pdb=" O ALA L 362 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER L 364 " --> pdb=" O SER L 350 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 16 through 21 removed outlier: 6.606A pdb=" N ALA L 35 " --> pdb=" O TYR L 17 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU L 19 " --> pdb=" O ALA L 33 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA L 33 " --> pdb=" O LEU L 19 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE L 21 " --> pdb=" O ARG L 31 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG L 31 " --> pdb=" O PHE L 21 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL L 41 " --> pdb=" O ASN L 61 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN L 61 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE L 43 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 74 removed outlier: 6.226A pdb=" N ILE L 90 " --> pdb=" O THR L 124 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR L 124 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU L 92 " --> pdb=" O VAL L 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 132 through 137 removed outlier: 6.220A pdb=" N ASP L 157 " --> pdb=" O LYS L 163 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS L 163 " --> pdb=" O ASP L 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 174 through 179 removed outlier: 3.617A pdb=" N GLY L 176 " --> pdb=" O LEU L 189 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU L 195 " --> pdb=" O ASN L 208 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN L 208 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL L 197 " --> pdb=" O ALA L 206 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG L 204 " --> pdb=" O SER L 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 211 through 213 Processing sheet with id=AB1, first strand: chain 'L' and resid 241 through 242 removed outlier: 3.822A pdb=" N ALA L 253 " --> pdb=" O THR L 265 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR L 265 " --> pdb=" O ALA L 253 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N CYS L 255 " --> pdb=" O MET L 263 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N MET L 263 " --> pdb=" O CYS L 255 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA L 279 " --> pdb=" O VAL L 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 288 through 299 removed outlier: 5.542A pdb=" N VAL L 318 " --> pdb=" O CYS L 294 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL L 296 " --> pdb=" O ARG L 316 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ARG L 316 " --> pdb=" O VAL L 296 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER L 326 " --> pdb=" O SER L 323 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 239 hydrogen bonds 438 hydrogen bond angles 0 basepair planarities 97 basepair parallelities 169 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.30 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: 2326 1.33 - 1.45: 3591 1.45 - 1.58: 5584 1.58 - 1.70: 430 1.70 - 1.82: 32 Bond restraints: 11963 Sorted by residual: bond pdb=" C3' DG I 25 " pdb=" C2' DG I 25 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" C3' DG J 124 " pdb=" C2' DG J 124 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DG J 69 " pdb=" C2' DG J 69 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG I 102 " pdb=" C2' DG I 102 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA I 60 " pdb=" C2' DA I 60 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 11958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 16744 2.30 - 4.59: 345 4.59 - 6.89: 27 6.89 - 9.18: 6 9.18 - 11.48: 1 Bond angle restraints: 17123 Sorted by residual: angle pdb=" C LEU G 65 " pdb=" N PRO G 66 " pdb=" CA PRO G 66 " ideal model delta sigma weight residual 118.85 127.59 -8.74 1.09e+00 8.42e-01 6.44e+01 angle pdb=" N LYS G 64 " pdb=" CA LYS G 64 " pdb=" C LYS G 64 " ideal model delta sigma weight residual 111.28 119.29 -8.01 1.09e+00 8.42e-01 5.40e+01 angle pdb=" CA LEU G 65 " pdb=" C LEU G 65 " pdb=" N PRO G 66 " ideal model delta sigma weight residual 120.93 116.13 4.80 1.06e+00 8.90e-01 2.05e+01 angle pdb=" N3 DT I 46 " pdb=" C4 DT I 46 " pdb=" O4 DT I 46 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" O4' DA I 65 " pdb=" C4' DA I 65 " pdb=" C3' DA I 65 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.99e+01 ... (remaining 17118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 5462 35.09 - 70.17: 1123 70.17 - 105.26: 37 105.26 - 140.34: 0 140.34 - 175.43: 4 Dihedral angle restraints: 6626 sinusoidal: 3721 harmonic: 2905 Sorted by residual: dihedral pdb=" CA PHE K 711 " pdb=" C PHE K 711 " pdb=" N LEU K 712 " pdb=" CA LEU K 712 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" C4' DC I 82 " pdb=" C3' DC I 82 " pdb=" O3' DC I 82 " pdb=" P DG I 83 " ideal model delta sinusoidal sigma weight residual 220.00 44.57 175.43 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC I 79 " pdb=" C3' DC I 79 " pdb=" O3' DC I 79 " pdb=" P DC I 80 " ideal model delta sinusoidal sigma weight residual -140.00 33.97 -173.97 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1497 0.049 - 0.097: 432 0.097 - 0.146: 87 0.146 - 0.194: 4 0.194 - 0.243: 1 Chirality restraints: 2021 Sorted by residual: chirality pdb=" CA LYS G 64 " pdb=" N LYS G 64 " pdb=" C LYS G 64 " pdb=" CB LYS G 64 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C3' DC I 79 " pdb=" C4' DC I 79 " pdb=" O3' DC I 79 " pdb=" C2' DC I 79 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" C3' DC I 82 " pdb=" C4' DC I 82 " pdb=" O3' DC I 82 " pdb=" C2' DC I 82 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 2018 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 63 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ARG G 63 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG G 63 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS G 64 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 82 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C LEU G 82 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU G 82 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG G 83 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU G 65 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO G 66 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 66 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 66 " -0.021 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1111 2.74 - 3.28: 10944 3.28 - 3.82: 21860 3.82 - 4.36: 23489 4.36 - 4.90: 34819 Nonbonded interactions: 92223 Sorted by model distance: nonbonded pdb=" O2 DC I 56 " pdb=" N2 DG J 92 " model vdw 2.200 2.496 nonbonded pdb=" N2 DG I 37 " pdb=" O2 DC J 111 " model vdw 2.219 2.496 nonbonded pdb=" O2 DC I 54 " pdb=" N2 DG J 94 " model vdw 2.231 2.496 nonbonded pdb=" N2 DG I 67 " pdb=" O2 DC J 81 " model vdw 2.239 2.496 nonbonded pdb=" OG1 THR E 118 " pdb=" NH1 ARG F 45 " model vdw 2.240 3.120 ... (remaining 92218 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 'C' and resid 59 through 134) selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 26 through 97) selection = (chain 'D' and resid 26 through 97) selection = (chain 'F' and resid 26 through 97) selection = (chain 'H' and resid 26 through 97) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.980 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11963 Z= 0.460 Angle : 0.798 11.477 17123 Z= 0.649 Chirality : 0.046 0.243 2021 Planarity : 0.004 0.048 1458 Dihedral : 28.445 175.426 4730 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.30 % Allowed : 34.39 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 974 helix: 0.66 (0.24), residues: 461 sheet: 0.40 (0.45), residues: 132 loop : -1.04 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 40 TYR 0.019 0.001 TYR C 99 PHE 0.022 0.001 PHE G 84 TRP 0.000 0.000 TRP K 690 HIS 0.009 0.003 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.46 (11963) covalent geometry : angle 0.79772 / 0.65 (17123) hydrogen bonds : bond 0.14707 / 9.81 ( 669) hydrogen bonds : angle 5.61335 / 3.88 ( 1689) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 236 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 LEU cc_start: 0.8749 (mt) cc_final: 0.8334 (mp) REVERT: F 88 TYR cc_start: 0.7381 (m-80) cc_final: 0.6741 (m-80) REVERT: D 68 ASP cc_start: 0.6511 (p0) cc_final: 0.5583 (p0) REVERT: D 77 LYS cc_start: 0.7997 (tptp) cc_final: 0.7788 (tppt) REVERT: A 90 MET cc_start: 0.8241 (mtm) cc_final: 0.7023 (mtm) outliers start: 7 outliers final: 0 residues processed: 239 average time/residue: 0.1395 time to fit residues: 44.6095 Evaluate side-chains 153 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** A 68 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 = 0.3737 r_free = 0.3737 target = 0.069279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.053716 restraints weight = 108385.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.055108 restraints weight = 52194.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055962 restraints weight = 33774.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.056311 restraints weight = 25862.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.056668 restraints weight = 22666.753| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11963 Z= 0.166 Angle : 0.742 8.601 17123 Z= 0.420 Chirality : 0.049 0.346 2021 Planarity : 0.005 0.060 1458 Dihedral : 30.725 176.769 3422 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.83 % Allowed : 32.16 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.26), residues: 974 helix: 0.54 (0.23), residues: 471 sheet: 0.24 (0.43), residues: 137 loop : -0.97 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 67 TYR 0.015 0.001 TYR F 88 PHE 0.017 0.002 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.009 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (11963) covalent geometry : angle 0.74216 / 0.42 (17123) hydrogen bonds : bond 0.07659 / 5.09 ( 669) hydrogen bonds : angle 4.34417 / 3.02 ( 1689) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 LEU cc_start: 0.9618 (tp) cc_final: 0.9119 (tp) REVERT: G 73 GLU cc_start: 0.7734 (tt0) cc_final: 0.7183 (mt-10) REVERT: G 78 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: G 84 PHE cc_start: 0.8801 (m-10) cc_final: 0.8523 (m-10) REVERT: H 63 GLU cc_start: 0.9060 (pp20) cc_final: 0.8807 (pp20) REVERT: H 88 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: E 64 LYS cc_start: 0.9533 (mmmm) cc_final: 0.9229 (mmmm) REVERT: E 67 PHE cc_start: 0.9163 (t80) cc_final: 0.8939 (t80) REVERT: E 90 MET cc_start: 0.9506 (tpp) cc_final: 0.9224 (mmp) REVERT: F 84 MET cc_start: 0.9155 (tpp) cc_final: 0.8442 (tpp) REVERT: F 88 TYR cc_start: 0.9460 (m-10) cc_final: 0.8864 (m-80) REVERT: C 74 ILE cc_start: 0.9751 (tt) cc_final: 0.9500 (tt) REVERT: C 94 GLU cc_start: 0.9160 (tp30) cc_final: 0.8254 (tp30) REVERT: D 25 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8505 (p0) REVERT: D 77 LYS cc_start: 0.9618 (tptp) cc_final: 0.9365 (tppt) REVERT: D 85 ASP cc_start: 0.8920 (m-30) cc_final: 0.8608 (t0) REVERT: A 90 MET cc_start: 0.8924 (mtm) cc_final: 0.8488 (mtm) REVERT: A 128 ARG cc_start: 0.9256 (mmm-85) cc_final: 0.8673 (mmm-85) REVERT: A 133 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8116 (mp0) outliers start: 26 outliers final: 11 residues processed: 204 average time/residue: 0.1190 time to fit residues: 33.7212 Evaluate side-chains 175 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain B residue 31 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.060353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.043715 restraints weight = 102477.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.044993 restraints weight = 54674.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.045775 restraints weight = 37330.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.046272 restraints weight = 29449.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.046426 restraints weight = 25486.586| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11963 Z= 0.231 Angle : 0.743 8.527 17123 Z= 0.419 Chirality : 0.048 0.321 2021 Planarity : 0.004 0.041 1458 Dihedral : 30.862 179.464 3422 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 7.25 % Allowed : 31.78 % Favored : 60.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.26), residues: 974 helix: 0.58 (0.23), residues: 469 sheet: 0.29 (0.43), residues: 137 loop : -1.06 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 134 TYR 0.009 0.001 TYR B 72 PHE 0.016 0.002 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.007 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.23 (11963) covalent geometry : angle 0.74312 / 0.42 (17123) hydrogen bonds : bond 0.07917 / 5.34 ( 669) hydrogen bonds : angle 4.25645 / 2.97 ( 1689) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 64 LYS cc_start: 0.9679 (OUTLIER) cc_final: 0.9472 (mtmm) REVERT: G 73 GLU cc_start: 0.7900 (tt0) cc_final: 0.7596 (mt-10) REVERT: H 88 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8513 (m-80) REVERT: E 64 LYS cc_start: 0.9577 (mmmm) cc_final: 0.9274 (mmmm) REVERT: E 90 MET cc_start: 0.9526 (tpp) cc_final: 0.9202 (mmp) REVERT: E 105 GLU cc_start: 0.9208 (tp30) cc_final: 0.8871 (mm-30) REVERT: F 84 MET cc_start: 0.9255 (tpp) cc_final: 0.8780 (tpp) REVERT: F 88 TYR cc_start: 0.9471 (m-10) cc_final: 0.9052 (m-80) REVERT: C 94 GLU cc_start: 0.8908 (tp30) cc_final: 0.8543 (tp30) REVERT: D 25 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8217 (p0) REVERT: D 26 ILE cc_start: 0.9721 (OUTLIER) cc_final: 0.9452 (tp) REVERT: D 77 LYS cc_start: 0.9659 (tptp) cc_final: 0.9429 (tppt) REVERT: D 91 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8674 (mmtm) REVERT: A 94 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8670 (mm-30) REVERT: A 120 MET cc_start: 0.8661 (mmm) cc_final: 0.8423 (mmt) REVERT: A 128 ARG cc_start: 0.9267 (mmm-85) cc_final: 0.9058 (mmm-85) REVERT: B 52 GLU cc_start: 0.9364 (pm20) cc_final: 0.9127 (pm20) REVERT: B 53 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8825 (mm-30) outliers start: 39 outliers final: 20 residues processed: 195 average time/residue: 0.1189 time to fit residues: 32.3243 Evaluate side-chains 178 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 85 optimal weight: 40.0000 chunk 89 optimal weight: 50.0000 chunk 79 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.067335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.051761 restraints weight = 109238.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.053125 restraints weight = 53328.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.053939 restraints weight = 34645.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.054353 restraints weight = 26700.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.054778 restraints weight = 23050.156| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11963 Z= 0.157 Angle : 0.705 8.743 17123 Z= 0.399 Chirality : 0.047 0.312 2021 Planarity : 0.004 0.041 1458 Dihedral : 30.931 178.220 3422 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.02 % Allowed : 34.76 % Favored : 60.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 974 helix: 0.66 (0.24), residues: 472 sheet: 0.39 (0.43), residues: 137 loop : -0.97 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 67 TYR 0.009 0.001 TYR C 99 PHE 0.017 0.002 PHE E 84 TRP 0.000 0.000 TRP K 690 HIS 0.008 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (11963) covalent geometry : angle 0.70510 / 0.40 (17123) hydrogen bonds : bond 0.06990 / 4.66 ( 669) hydrogen bonds : angle 3.99772 / 2.79 ( 1689) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 LEU cc_start: 0.9710 (tp) cc_final: 0.9188 (mt) REVERT: G 73 GLU cc_start: 0.8132 (tt0) cc_final: 0.7512 (mt-10) REVERT: G 84 PHE cc_start: 0.8752 (m-10) cc_final: 0.8364 (m-10) REVERT: G 120 MET cc_start: 0.9089 (mmt) cc_final: 0.8821 (mmm) REVERT: H 88 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: E 59 GLU cc_start: 0.9091 (pm20) cc_final: 0.8844 (pm20) REVERT: E 64 LYS cc_start: 0.9585 (mmmm) cc_final: 0.9181 (mmmm) REVERT: E 68 GLN cc_start: 0.9654 (mt0) cc_final: 0.9380 (tp40) REVERT: E 90 MET cc_start: 0.9507 (tpp) cc_final: 0.9137 (mmp) REVERT: E 105 GLU cc_start: 0.9186 (tp30) cc_final: 0.8884 (mm-30) REVERT: E 120 MET cc_start: 0.9223 (mmm) cc_final: 0.8988 (mmm) REVERT: F 84 MET cc_start: 0.9246 (tpp) cc_final: 0.8683 (tpp) REVERT: F 88 TYR cc_start: 0.9453 (m-10) cc_final: 0.8994 (m-80) REVERT: C 94 GLU cc_start: 0.8935 (tp30) cc_final: 0.8485 (tp30) REVERT: C 105 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9126 (mm-30) REVERT: D 26 ILE cc_start: 0.9672 (OUTLIER) cc_final: 0.9432 (tp) REVERT: D 53 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8709 (tm-30) REVERT: D 77 LYS cc_start: 0.9647 (tptp) cc_final: 0.9434 (tppt) REVERT: D 85 ASP cc_start: 0.8922 (m-30) cc_final: 0.8671 (t0) REVERT: D 91 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8586 (mptt) REVERT: A 94 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8656 (mm-30) REVERT: A 128 ARG cc_start: 0.9296 (mmm-85) cc_final: 0.8543 (mmm-85) REVERT: B 53 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8749 (mt-10) outliers start: 27 outliers final: 14 residues processed: 189 average time/residue: 0.1194 time to fit residues: 31.4475 Evaluate side-chains 173 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 108 optimal weight: 50.0000 chunk 115 optimal weight: 0.0470 chunk 78 optimal weight: 30.0000 chunk 19 optimal weight: 0.5980 chunk 87 optimal weight: 50.0000 chunk 3 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 90 optimal weight: 50.0000 chunk 75 optimal weight: 10.0000 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.067386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.051828 restraints weight = 109345.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.053093 restraints weight = 54425.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.053904 restraints weight = 35316.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.054349 restraints weight = 27237.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.054791 restraints weight = 23227.986| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11963 Z= 0.151 Angle : 0.714 10.755 17123 Z= 0.400 Chirality : 0.048 0.393 2021 Planarity : 0.004 0.044 1458 Dihedral : 30.909 177.944 3422 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.39 % Allowed : 35.13 % Favored : 59.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 974 helix: 0.58 (0.23), residues: 478 sheet: 0.46 (0.43), residues: 142 loop : -0.85 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 92 TYR 0.011 0.001 TYR C 99 PHE 0.016 0.002 PHE A 67 TRP 0.000 0.000 TRP K 690 HIS 0.007 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (11963) covalent geometry : angle 0.71421 / 0.40 (17123) hydrogen bonds : bond 0.06877 / 4.60 ( 669) hydrogen bonds : angle 3.93754 / 2.76 ( 1689) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 LEU cc_start: 0.9706 (tp) cc_final: 0.9151 (mt) REVERT: G 73 GLU cc_start: 0.8067 (tt0) cc_final: 0.7487 (mt-10) REVERT: G 84 PHE cc_start: 0.8711 (m-10) cc_final: 0.8299 (m-10) REVERT: H 88 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: E 50 GLU cc_start: 0.8764 (tp30) cc_final: 0.8379 (tp30) REVERT: E 64 LYS cc_start: 0.9589 (mmmm) cc_final: 0.9208 (mmmm) REVERT: E 90 MET cc_start: 0.9503 (tpp) cc_final: 0.9126 (mmp) REVERT: E 105 GLU cc_start: 0.9191 (tp30) cc_final: 0.8928 (mm-30) REVERT: E 120 MET cc_start: 0.9202 (mmm) cc_final: 0.8978 (mmm) REVERT: F 63 GLU cc_start: 0.8948 (tp30) cc_final: 0.8608 (tp30) REVERT: F 84 MET cc_start: 0.9193 (tpp) cc_final: 0.8594 (tpp) REVERT: F 88 TYR cc_start: 0.9422 (m-10) cc_final: 0.8949 (m-80) REVERT: C 105 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9136 (mm-30) REVERT: D 53 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8703 (tm-30) REVERT: D 77 LYS cc_start: 0.9638 (tptp) cc_final: 0.9428 (tppt) REVERT: D 85 ASP cc_start: 0.8878 (m-30) cc_final: 0.8670 (t0) REVERT: D 91 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8539 (mptt) REVERT: A 78 PHE cc_start: 0.8728 (m-10) cc_final: 0.8085 (m-10) REVERT: A 90 MET cc_start: 0.9005 (mtm) cc_final: 0.8723 (mtm) REVERT: A 94 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8606 (mm-30) REVERT: A 120 MET cc_start: 0.8133 (mmt) cc_final: 0.7708 (mmm) REVERT: A 128 ARG cc_start: 0.9333 (mmm-85) cc_final: 0.8442 (mmm-85) REVERT: A 133 GLU cc_start: 0.8378 (mp0) cc_final: 0.7474 (mp0) REVERT: B 52 GLU cc_start: 0.9337 (pm20) cc_final: 0.9046 (pm20) REVERT: B 53 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8820 (mm-30) outliers start: 29 outliers final: 19 residues processed: 190 average time/residue: 0.1188 time to fit residues: 31.5651 Evaluate side-chains 180 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 114 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 chunk 69 optimal weight: 40.0000 chunk 80 optimal weight: 50.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.052153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.036400 restraints weight = 81552.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.037436 restraints weight = 45156.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.038164 restraints weight = 31402.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.038652 restraints weight = 24768.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.038960 restraints weight = 21201.510| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11963 Z= 0.222 Angle : 0.753 8.801 17123 Z= 0.420 Chirality : 0.048 0.306 2021 Planarity : 0.004 0.035 1458 Dihedral : 31.094 178.899 3422 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 6.32 % Allowed : 34.57 % Favored : 59.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 974 helix: 0.51 (0.23), residues: 475 sheet: 0.66 (0.44), residues: 135 loop : -0.80 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 67 TYR 0.020 0.002 TYR E 54 PHE 0.036 0.003 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.005 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.22 (11963) covalent geometry : angle 0.75278 / 0.42 (17123) hydrogen bonds : bond 0.08083 / 5.47 ( 669) hydrogen bonds : angle 4.07354 / 2.84 ( 1689) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 GLU cc_start: 0.8134 (tt0) cc_final: 0.7548 (mt-10) REVERT: G 125 GLN cc_start: 0.9485 (mt0) cc_final: 0.9134 (mm-40) REVERT: H 88 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: E 59 GLU cc_start: 0.9385 (pm20) cc_final: 0.9172 (pm20) REVERT: E 64 LYS cc_start: 0.9628 (mmmm) cc_final: 0.9262 (mmmm) REVERT: E 90 MET cc_start: 0.9469 (tpp) cc_final: 0.9052 (mmp) REVERT: E 120 MET cc_start: 0.9232 (mmm) cc_final: 0.8995 (mmm) REVERT: F 63 GLU cc_start: 0.9050 (tp30) cc_final: 0.8728 (tp30) REVERT: F 84 MET cc_start: 0.9257 (tpp) cc_final: 0.8718 (tpp) REVERT: F 88 TYR cc_start: 0.9482 (m-10) cc_final: 0.9103 (m-80) REVERT: C 94 GLU cc_start: 0.9045 (tp30) cc_final: 0.8814 (tp30) REVERT: C 105 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9174 (mm-30) REVERT: D 53 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8853 (tm-30) REVERT: D 77 LYS cc_start: 0.9681 (tptp) cc_final: 0.9439 (tppt) REVERT: D 84 MET cc_start: 0.8923 (tpp) cc_final: 0.8575 (tmm) REVERT: D 85 ASP cc_start: 0.8978 (m-30) cc_final: 0.8637 (t0) REVERT: A 78 PHE cc_start: 0.8298 (m-10) cc_final: 0.8032 (m-80) REVERT: A 90 MET cc_start: 0.8984 (mtm) cc_final: 0.8592 (mtm) REVERT: A 94 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8682 (mm-30) REVERT: A 120 MET cc_start: 0.8315 (mmt) cc_final: 0.7810 (mmm) REVERT: B 66 ILE cc_start: 0.9067 (pt) cc_final: 0.8523 (mm) outliers start: 34 outliers final: 20 residues processed: 183 average time/residue: 0.1191 time to fit residues: 30.3678 Evaluate side-chains 173 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 40.0000 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.052879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035948 restraints weight = 87885.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.037075 restraints weight = 48943.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.037774 restraints weight = 34289.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.038221 restraints weight = 27514.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.038498 restraints weight = 23982.248| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11963 Z= 0.185 Angle : 0.738 11.755 17123 Z= 0.413 Chirality : 0.048 0.276 2021 Planarity : 0.004 0.044 1458 Dihedral : 31.161 176.796 3422 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.58 % Allowed : 36.80 % Favored : 57.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 974 helix: 0.62 (0.23), residues: 475 sheet: 0.66 (0.43), residues: 142 loop : -0.77 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 128 TYR 0.011 0.001 TYR C 99 PHE 0.074 0.003 PHE A 78 TRP 0.000 0.000 TRP K 690 HIS 0.006 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (11963) covalent geometry : angle 0.73820 / 0.41 (17123) hydrogen bonds : bond 0.07040 / 4.73 ( 669) hydrogen bonds : angle 4.04026 / 2.82 ( 1689) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 LEU cc_start: 0.9732 (tp) cc_final: 0.9172 (mt) REVERT: G 73 GLU cc_start: 0.8133 (tt0) cc_final: 0.7518 (mt-10) REVERT: G 84 PHE cc_start: 0.8724 (m-10) cc_final: 0.8345 (m-10) REVERT: G 125 GLN cc_start: 0.9485 (mt0) cc_final: 0.9152 (mm-40) REVERT: H 59 LYS cc_start: 0.9645 (tppt) cc_final: 0.9438 (mmmm) REVERT: H 88 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8515 (m-80) REVERT: E 54 TYR cc_start: 0.8455 (m-80) cc_final: 0.8076 (m-10) REVERT: E 64 LYS cc_start: 0.9614 (OUTLIER) cc_final: 0.9257 (mmmm) REVERT: E 68 GLN cc_start: 0.9675 (tt0) cc_final: 0.9367 (tp-100) REVERT: E 90 MET cc_start: 0.9471 (tpp) cc_final: 0.9088 (mmp) REVERT: E 120 MET cc_start: 0.9207 (mmm) cc_final: 0.8965 (mmm) REVERT: F 84 MET cc_start: 0.9210 (tpp) cc_final: 0.8638 (tpp) REVERT: F 88 TYR cc_start: 0.9435 (m-10) cc_final: 0.9033 (m-80) REVERT: C 94 GLU cc_start: 0.9021 (tp30) cc_final: 0.8765 (tp30) REVERT: C 105 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9189 (mm-30) REVERT: D 53 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8757 (tm-30) REVERT: D 77 LYS cc_start: 0.9679 (tptp) cc_final: 0.9441 (tppt) REVERT: D 91 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8670 (mmtt) REVERT: A 90 MET cc_start: 0.8978 (mtm) cc_final: 0.8559 (mtm) REVERT: A 94 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8680 (mm-30) REVERT: A 120 MET cc_start: 0.8269 (mmt) cc_final: 0.7813 (mmm) REVERT: B 52 GLU cc_start: 0.9408 (pm20) cc_final: 0.9071 (pm20) REVERT: B 53 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8881 (mm-30) outliers start: 30 outliers final: 20 residues processed: 181 average time/residue: 0.1135 time to fit residues: 28.7082 Evaluate side-chains 176 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 40.0000 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 112 optimal weight: 30.0000 chunk 79 optimal weight: 50.0000 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.053136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.036815 restraints weight = 82677.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.037977 restraints weight = 45551.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.038709 restraints weight = 31550.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.039167 restraints weight = 24975.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.039480 restraints weight = 21637.052| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11963 Z= 0.159 Angle : 0.764 16.032 17123 Z= 0.415 Chirality : 0.049 0.442 2021 Planarity : 0.004 0.029 1458 Dihedral : 31.116 176.094 3422 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.46 % Allowed : 38.10 % Favored : 57.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.27), residues: 974 helix: 0.67 (0.23), residues: 475 sheet: 0.70 (0.43), residues: 145 loop : -0.78 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 128 TYR 0.014 0.001 TYR B 72 PHE 0.022 0.002 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (11963) covalent geometry : angle 0.76440 / 0.41 (17123) hydrogen bonds : bond 0.06724 / 4.51 ( 669) hydrogen bonds : angle 3.97307 / 2.78 ( 1689) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 LEU cc_start: 0.9723 (tp) cc_final: 0.9156 (mt) REVERT: G 73 GLU cc_start: 0.8098 (tt0) cc_final: 0.7487 (mt-10) REVERT: G 84 PHE cc_start: 0.8664 (m-10) cc_final: 0.8271 (m-10) REVERT: H 88 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8450 (m-80) REVERT: E 64 LYS cc_start: 0.9608 (OUTLIER) cc_final: 0.9249 (mmmm) REVERT: E 68 GLN cc_start: 0.9679 (tt0) cc_final: 0.9293 (tp-100) REVERT: E 90 MET cc_start: 0.9448 (tpp) cc_final: 0.9085 (mmp) REVERT: E 105 GLU cc_start: 0.9196 (tp30) cc_final: 0.8940 (mm-30) REVERT: F 40 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8072 (tpp80) REVERT: F 84 MET cc_start: 0.9218 (tpp) cc_final: 0.8584 (tpp) REVERT: F 88 TYR cc_start: 0.9418 (m-10) cc_final: 0.8971 (m-80) REVERT: C 94 GLU cc_start: 0.9017 (tp30) cc_final: 0.8679 (tp30) REVERT: C 105 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9195 (mm-30) REVERT: D 53 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8716 (tm-30) REVERT: D 77 LYS cc_start: 0.9672 (tptp) cc_final: 0.9426 (tppt) REVERT: D 91 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8638 (mmtt) REVERT: A 90 MET cc_start: 0.9016 (mtm) cc_final: 0.8526 (mtm) REVERT: A 94 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8667 (mm-30) REVERT: A 97 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8943 (pp20) REVERT: A 120 MET cc_start: 0.8333 (mmt) cc_final: 0.7873 (mmm) REVERT: B 52 GLU cc_start: 0.9399 (pm20) cc_final: 0.9021 (pm20) REVERT: B 53 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8821 (mm-30) outliers start: 24 outliers final: 18 residues processed: 176 average time/residue: 0.1228 time to fit residues: 29.8022 Evaluate side-chains 174 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 50.0000 chunk 94 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 95 optimal weight: 0.0020 chunk 111 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 72 optimal weight: 30.0000 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.051951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.036248 restraints weight = 81993.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.037321 restraints weight = 45271.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.038063 restraints weight = 31284.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.038544 restraints weight = 24645.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.038848 restraints weight = 21146.824| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11963 Z= 0.192 Angle : 0.755 13.836 17123 Z= 0.416 Chirality : 0.048 0.390 2021 Planarity : 0.004 0.025 1458 Dihedral : 31.172 177.135 3422 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.83 % Allowed : 37.55 % Favored : 57.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.27), residues: 974 helix: 0.63 (0.23), residues: 478 sheet: 0.57 (0.43), residues: 147 loop : -0.81 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 131 TYR 0.013 0.001 TYR B 72 PHE 0.023 0.002 PHE A 67 TRP 0.000 0.000 TRP K 690 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (11963) covalent geometry : angle 0.75546 / 0.42 (17123) hydrogen bonds : bond 0.07156 / 4.82 ( 669) hydrogen bonds : angle 4.03937 / 2.83 ( 1689) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 LEU cc_start: 0.9740 (tp) cc_final: 0.9191 (mt) REVERT: G 73 GLU cc_start: 0.8182 (tt0) cc_final: 0.7583 (mt-10) REVERT: G 84 PHE cc_start: 0.8655 (m-10) cc_final: 0.8231 (m-10) REVERT: G 120 MET cc_start: 0.9097 (mmt) cc_final: 0.8856 (mmm) REVERT: H 88 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: E 64 LYS cc_start: 0.9622 (OUTLIER) cc_final: 0.9259 (mmmm) REVERT: E 68 GLN cc_start: 0.9707 (tt0) cc_final: 0.9317 (tp-100) REVERT: E 90 MET cc_start: 0.9469 (tpp) cc_final: 0.9056 (mmp) REVERT: E 105 GLU cc_start: 0.9201 (tp30) cc_final: 0.8996 (tp30) REVERT: F 40 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.8275 (tpp80) REVERT: F 63 GLU cc_start: 0.8795 (tp30) cc_final: 0.8527 (tp30) REVERT: F 84 MET cc_start: 0.9250 (tpp) cc_final: 0.8668 (tpp) REVERT: F 88 TYR cc_start: 0.9457 (m-10) cc_final: 0.9081 (m-80) REVERT: C 105 GLU cc_start: 0.9478 (mm-30) cc_final: 0.9222 (mm-30) REVERT: D 53 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8784 (tm-30) REVERT: D 77 LYS cc_start: 0.9683 (tptp) cc_final: 0.9448 (tppt) REVERT: D 91 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8562 (mptt) REVERT: A 90 MET cc_start: 0.9013 (mtm) cc_final: 0.8796 (mmm) REVERT: A 94 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8699 (mm-30) REVERT: A 120 MET cc_start: 0.8471 (mmt) cc_final: 0.8042 (mmm) outliers start: 26 outliers final: 22 residues processed: 174 average time/residue: 0.1144 time to fit residues: 27.8063 Evaluate side-chains 174 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 21 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 30.0000 chunk 2 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.052544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.036810 restraints weight = 82505.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.037975 restraints weight = 44731.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.038731 restraints weight = 30610.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.039208 restraints weight = 24008.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.039539 restraints weight = 20606.047| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11963 Z= 0.158 Angle : 0.751 14.485 17123 Z= 0.411 Chirality : 0.048 0.382 2021 Planarity : 0.004 0.031 1458 Dihedral : 31.172 175.759 3422 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.65 % Allowed : 38.29 % Favored : 57.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.27), residues: 974 helix: 0.65 (0.23), residues: 478 sheet: 0.65 (0.43), residues: 147 loop : -0.76 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.012 0.001 TYR B 72 PHE 0.019 0.002 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (11963) covalent geometry : angle 0.75122 / 0.41 (17123) hydrogen bonds : bond 0.06618 / 4.42 ( 669) hydrogen bonds : angle 3.94357 / 2.78 ( 1689) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 LEU cc_start: 0.9728 (tp) cc_final: 0.9141 (mt) REVERT: G 73 GLU cc_start: 0.8154 (tt0) cc_final: 0.7559 (mt-10) REVERT: G 82 LEU cc_start: 0.8071 (mm) cc_final: 0.7693 (mm) REVERT: G 84 PHE cc_start: 0.8604 (m-10) cc_final: 0.8152 (m-10) REVERT: H 44 LYS cc_start: 0.9558 (tppp) cc_final: 0.9036 (tppt) REVERT: H 88 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: E 64 LYS cc_start: 0.9615 (OUTLIER) cc_final: 0.9253 (mmmm) REVERT: E 68 GLN cc_start: 0.9700 (tt0) cc_final: 0.9311 (tp-100) REVERT: E 90 MET cc_start: 0.9462 (tpp) cc_final: 0.9057 (mmp) REVERT: E 105 GLU cc_start: 0.9175 (tp30) cc_final: 0.8964 (tp30) REVERT: F 84 MET cc_start: 0.9245 (tpp) cc_final: 0.8637 (tpp) REVERT: F 88 TYR cc_start: 0.9457 (m-10) cc_final: 0.9052 (m-80) REVERT: C 105 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9211 (mm-30) REVERT: D 77 LYS cc_start: 0.9664 (tptp) cc_final: 0.9432 (tppt) REVERT: D 91 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8597 (mmtt) REVERT: A 90 MET cc_start: 0.9023 (mtm) cc_final: 0.8790 (mmm) REVERT: A 94 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8682 (mm-30) REVERT: A 97 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8937 (pp20) REVERT: A 120 MET cc_start: 0.8475 (mmt) cc_final: 0.8065 (mmm) REVERT: B 53 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8896 (mm-30) outliers start: 25 outliers final: 21 residues processed: 172 average time/residue: 0.1163 time to fit residues: 27.8696 Evaluate side-chains 173 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 40.0000 chunk 44 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 chunk 100 optimal weight: 50.0000 chunk 17 optimal weight: 0.8980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.066325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.050881 restraints weight = 109842.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.052236 restraints weight = 53910.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.053060 restraints weight = 35145.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.053492 restraints weight = 26966.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.053871 restraints weight = 23145.544| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11963 Z= 0.151 Angle : 0.762 14.561 17123 Z= 0.414 Chirality : 0.048 0.384 2021 Planarity : 0.004 0.032 1458 Dihedral : 31.022 175.339 3422 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.09 % Allowed : 38.29 % Favored : 57.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.27), residues: 974 helix: 0.59 (0.23), residues: 478 sheet: 0.75 (0.44), residues: 147 loop : -0.77 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 128 TYR 0.010 0.001 TYR B 72 PHE 0.019 0.002 PHE A 67 TRP 0.000 0.000 TRP K 690 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (11963) covalent geometry : angle 0.76192 / 0.41 (17123) hydrogen bonds : bond 0.06707 / 4.46 ( 669) hydrogen bonds : angle 3.87498 / 2.73 ( 1689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2400.44 seconds wall clock time: 41 minutes 58.29 seconds (2518.29 seconds total)