Starting phenix.real_space_refine on Wed Mar 4 09:42:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y60_33630/03_2026/7y60_33630.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y60_33630/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y60_33630/03_2026/7y60_33630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y60_33630/03_2026/7y60_33630.map" model { file = "/net/cci-nas-00/data/ceres_data/7y60_33630/03_2026/7y60_33630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y60_33630/03_2026/7y60_33630.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.54, per 1000 atoms: 0.22 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 410.7 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: 1.63 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: 2.17 Time building geometry restraints manager: 1.25 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=" C ARG G 63 " pdb=" O ARG G 63 " ideal model delta sigma weight residual 1.234 1.210 0.025 1.20e-02 6.94e+03 4.27e+00 bond pdb=" N ARG G 63 " pdb=" CA ARG G 63 " ideal model delta sigma weight residual 1.456 1.479 -0.022 1.28e-02 6.10e+03 3.09e+00 bond pdb=" CD ARG G 63 " pdb=" NE ARG G 63 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.40e-02 5.10e+03 2.87e+00 bond pdb=" C LEU G 65 " pdb=" O LEU G 65 " ideal model delta sigma weight residual 1.244 1.229 0.014 9.80e-03 1.04e+04 2.17e+00 bond pdb=" C3' DC I 79 " pdb=" O3' DC I 79 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.05e+00 ... (remaining 11958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 16916 2.30 - 4.59: 173 4.59 - 6.89: 26 6.89 - 9.18: 7 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=" O3' DC I 84 " pdb=" C3' DC I 84 " pdb=" C2' DC I 84 " ideal model delta sigma weight residual 111.50 102.59 8.91 1.50e+00 4.44e-01 3.53e+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=" C ARG G 63 " pdb=" CA ARG G 63 " pdb=" CB ARG G 63 " ideal model delta sigma weight residual 109.90 116.83 -6.93 1.56e+00 4.11e-01 1.97e+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: 1657 0.049 - 0.097: 294 0.097 - 0.146: 66 0.146 - 0.194: 3 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=" CG LEU F 37 " pdb=" CB LEU F 37 " pdb=" CD1 LEU F 37 " pdb=" CD2 LEU F 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" C3' DC I 84 " pdb=" C4' DC I 84 " pdb=" O3' DC I 84 " pdb=" C2' DC I 84 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.38e-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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.040 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 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 : 0.004 0.043 11963 Z= 0.170 Angle : 0.674 11.477 17123 Z= 0.397 Chirality : 0.040 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 covalent geometry : bond 0.00360 (11963) covalent geometry : angle 0.67430 (17123) hydrogen bonds : bond 0.14707 ( 669) hydrogen bonds : angle 5.61335 ( 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 : 0.267 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: 0.5585 (p0) REVERT: D 77 LYS cc_start: 0.7997 (tptp) cc_final: 0.7789 (tppt) REVERT: A 90 MET cc_start: 0.8241 (mtm) cc_final: 0.7022 (mtm) outliers start: 7 outliers final: 0 residues processed: 239 average time/residue: 0.1303 time to fit residues: 41.2320 Evaluate side-chains 152 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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: 9.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 40.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 27 GLN ** 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 = 0.3660 r_free = 0.3660 target = 0.065041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.049221 restraints weight = 110911.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.050542 restraints weight = 54653.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.051342 restraints weight = 35813.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.051750 restraints weight = 27733.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.052101 restraints weight = 23838.727| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11963 Z= 0.255 Angle : 0.695 8.755 17123 Z= 0.397 Chirality : 0.042 0.185 2021 Planarity : 0.004 0.037 1458 Dihedral : 30.898 177.876 3422 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.69 % Allowed : 30.86 % Favored : 62.45 % 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: 0.29 (0.26), residues: 974 helix: 0.90 (0.24), residues: 476 sheet: 0.51 (0.43), residues: 137 loop : -0.79 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 128 TYR 0.015 0.001 TYR C 99 PHE 0.023 0.002 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.010 0.003 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00552 (11963) covalent geometry : angle 0.69544 (17123) hydrogen bonds : bond 0.07501 ( 669) hydrogen bonds : angle 4.06076 ( 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 221 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.247 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 60 LEU cc_start: 0.8890 (pt) cc_final: 0.8679 (pp) REVERT: G 62 ILE cc_start: 0.9626 (mp) cc_final: 0.9361 (pt) REVERT: G 73 GLU cc_start: 0.7860 (tt0) cc_final: 0.7606 (mt-10) REVERT: G 84 PHE cc_start: 0.8940 (m-10) cc_final: 0.8603 (m-10) REVERT: G 90 MET cc_start: 0.8549 (tmm) cc_final: 0.8176 (tmm) REVERT: H 26 ILE cc_start: 0.9705 (OUTLIER) cc_final: 0.9382 (mm) REVERT: H 27 GLN cc_start: 0.9466 (mp10) cc_final: 0.9011 (pm20) REVERT: H 63 GLU cc_start: 0.8988 (pp20) cc_final: 0.8708 (pp20) REVERT: H 88 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8584 (m-80) REVERT: E 60 LEU cc_start: 0.9187 (mt) cc_final: 0.8982 (mt) REVERT: E 64 LYS cc_start: 0.9583 (mmmm) cc_final: 0.9382 (mmmm) REVERT: F 63 GLU cc_start: 0.9004 (tp30) cc_final: 0.8413 (tp30) REVERT: F 67 ARG cc_start: 0.8360 (ttm110) cc_final: 0.7886 (ttm110) REVERT: F 84 MET cc_start: 0.9275 (tpp) cc_final: 0.8754 (tpp) REVERT: F 88 TYR cc_start: 0.9400 (m-80) cc_final: 0.8763 (m-80) REVERT: C 54 TYR cc_start: 0.9140 (m-80) cc_final: 0.8870 (m-80) REVERT: C 74 ILE cc_start: 0.9765 (tt) cc_final: 0.9564 (tt) REVERT: C 80 THR cc_start: 0.9027 (m) cc_final: 0.8494 (m) REVERT: C 94 GLU cc_start: 0.9321 (tp30) cc_final: 0.8127 (tp30) REVERT: D 25 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8733 (p0) REVERT: D 63 GLU cc_start: 0.9181 (tp30) cc_final: 0.8961 (mm-30) REVERT: D 77 LYS cc_start: 0.9667 (tptp) cc_final: 0.9453 (tppt) REVERT: D 84 MET cc_start: 0.8951 (tpp) cc_final: 0.8356 (tmm) REVERT: A 90 MET cc_start: 0.8795 (mtm) cc_final: 0.8263 (mtm) REVERT: A 94 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8685 (mm-30) REVERT: A 128 ARG cc_start: 0.9260 (mmm-85) cc_final: 0.8509 (mmm-85) REVERT: A 133 GLU cc_start: 0.8560 (mm-30) cc_final: 0.7998 (mp0) REVERT: B 53 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8582 (mm-30) outliers start: 36 outliers final: 20 residues processed: 210 average time/residue: 0.1166 time to fit residues: 33.5925 Evaluate side-chains 181 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 89 VAL 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 66 ILE Chi-restraints excluded: chain F residue 86 VAL 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 0.0000 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 27 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.066894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.051356 restraints weight = 108827.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.052702 restraints weight = 53193.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.053407 restraints weight = 34489.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.054014 restraints weight = 26747.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.054262 restraints weight = 22734.862| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11963 Z= 0.160 Angle : 0.653 11.730 17123 Z= 0.369 Chirality : 0.040 0.182 2021 Planarity : 0.003 0.037 1458 Dihedral : 30.772 178.389 3422 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.20 % Allowed : 32.71 % Favored : 62.08 % 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: 0.49 (0.26), residues: 974 helix: 1.03 (0.24), residues: 475 sheet: 0.70 (0.43), residues: 145 loop : -0.73 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 67 TYR 0.010 0.001 TYR B 72 PHE 0.013 0.001 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.008 0.002 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00344 (11963) covalent geometry : angle 0.65336 (17123) hydrogen bonds : bond 0.06387 ( 669) hydrogen bonds : angle 3.74213 ( 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 204 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.381 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: G 73 GLU cc_start: 0.8172 (tt0) cc_final: 0.7612 (mt-10) REVERT: G 84 PHE cc_start: 0.8620 (m-10) cc_final: 0.8174 (m-10) REVERT: H 44 LYS cc_start: 0.9262 (tppt) cc_final: 0.9053 (tppt) REVERT: H 88 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: E 64 LYS cc_start: 0.9609 (mmmm) cc_final: 0.9297 (mmmm) REVERT: E 68 GLN cc_start: 0.9681 (tt0) cc_final: 0.9322 (tp-100) REVERT: E 120 MET cc_start: 0.9281 (mmm) cc_final: 0.8981 (mmm) REVERT: F 53 GLU cc_start: 0.8868 (tp30) cc_final: 0.8541 (tp30) REVERT: F 63 GLU cc_start: 0.9126 (tp30) cc_final: 0.8885 (tp30) REVERT: F 84 MET cc_start: 0.9212 (tpp) cc_final: 0.8617 (tpp) REVERT: F 88 TYR cc_start: 0.9374 (m-80) cc_final: 0.8700 (m-80) REVERT: C 94 GLU cc_start: 0.8729 (tp30) cc_final: 0.8240 (tp30) REVERT: C 105 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9160 (mm-30) REVERT: D 25 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8224 (p0) REVERT: D 26 ILE cc_start: 0.9732 (OUTLIER) cc_final: 0.9449 (tp) REVERT: D 63 GLU cc_start: 0.9152 (tp30) cc_final: 0.8920 (mm-30) REVERT: D 77 LYS cc_start: 0.9633 (tptp) cc_final: 0.9417 (tppt) REVERT: A 78 PHE cc_start: 0.9318 (t80) cc_final: 0.9103 (t80) REVERT: A 90 MET cc_start: 0.8882 (mtm) cc_final: 0.8224 (mtm) REVERT: A 94 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8697 (mm-30) REVERT: A 97 GLU cc_start: 0.9283 (tm-30) cc_final: 0.9079 (pp20) REVERT: A 128 ARG cc_start: 0.9263 (mmm-85) cc_final: 0.8362 (mmm-85) REVERT: A 133 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8309 (mp0) REVERT: B 52 GLU cc_start: 0.9310 (pm20) cc_final: 0.9089 (pm20) REVERT: B 53 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8733 (mm-30) REVERT: B 63 GLU cc_start: 0.9631 (tp30) cc_final: 0.9347 (tp30) outliers start: 28 outliers final: 11 residues processed: 197 average time/residue: 0.1125 time to fit residues: 30.6907 Evaluate side-chains 166 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 100 LEU 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 125 GLN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 85 optimal weight: 50.0000 chunk 89 optimal weight: 50.0000 chunk 79 optimal weight: 0.0670 chunk 105 optimal weight: 4.9990 chunk 100 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS D 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.053688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.037791 restraints weight = 80939.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.038949 restraints weight = 44580.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.039713 restraints weight = 30607.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.040216 restraints weight = 24092.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.040546 restraints weight = 20496.712| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11963 Z= 0.165 Angle : 0.647 13.083 17123 Z= 0.364 Chirality : 0.040 0.269 2021 Planarity : 0.003 0.030 1458 Dihedral : 30.756 178.817 3422 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.95 % Allowed : 34.01 % Favored : 60.04 % 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: 0.60 (0.27), residues: 974 helix: 1.10 (0.24), residues: 475 sheet: 0.80 (0.43), residues: 145 loop : -0.66 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.013 0.001 TYR E 54 PHE 0.013 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 covalent geometry : bond 0.00361 (11963) covalent geometry : angle 0.64736 (17123) hydrogen bonds : bond 0.06287 ( 669) hydrogen bonds : angle 3.68218 ( 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 201 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.369 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: G 70 LEU cc_start: 0.9713 (tp) cc_final: 0.9198 (mt) REVERT: G 73 GLU cc_start: 0.8087 (tt0) cc_final: 0.7546 (mt-10) REVERT: G 84 PHE cc_start: 0.8654 (m-10) cc_final: 0.8155 (m-10) REVERT: H 44 LYS cc_start: 0.9398 (tppt) cc_final: 0.9163 (tptp) REVERT: H 88 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8474 (m-80) REVERT: E 64 LYS cc_start: 0.9637 (mmmm) cc_final: 0.9308 (mmmm) REVERT: E 68 GLN cc_start: 0.9706 (tt0) cc_final: 0.9371 (tp40) REVERT: F 84 MET cc_start: 0.9293 (tpp) cc_final: 0.8658 (tpp) REVERT: F 88 TYR cc_start: 0.9468 (m-80) cc_final: 0.8806 (m-80) REVERT: C 94 GLU cc_start: 0.8809 (tp30) cc_final: 0.8360 (tp30) REVERT: C 97 GLU cc_start: 0.8113 (pp20) cc_final: 0.7843 (pp20) REVERT: C 105 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9229 (mm-30) REVERT: C 120 MET cc_start: 0.9355 (mtp) cc_final: 0.9142 (mmm) REVERT: D 25 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7880 (p0) REVERT: D 63 GLU cc_start: 0.9283 (tp30) cc_final: 0.8972 (mm-30) REVERT: D 77 LYS cc_start: 0.9637 (tptp) cc_final: 0.9382 (tppt) REVERT: D 91 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8481 (mmtm) REVERT: A 90 MET cc_start: 0.8880 (mtm) cc_final: 0.8393 (mtm) REVERT: A 94 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8579 (mm-30) REVERT: A 120 MET cc_start: 0.8244 (mmt) cc_final: 0.7885 (mmm) REVERT: B 52 GLU cc_start: 0.9317 (pm20) cc_final: 0.9101 (pm20) REVERT: B 53 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8793 (mm-30) REVERT: B 64 ASN cc_start: 0.9669 (m-40) cc_final: 0.9458 (p0) outliers start: 32 outliers final: 14 residues processed: 194 average time/residue: 0.1187 time to fit residues: 31.5964 Evaluate side-chains 168 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 LEU 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 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 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 25 ASN 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 95 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 0.0970 chunk 115 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 87 optimal weight: 50.0000 chunk 3 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** 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 = 0.3691 r_free = 0.3691 target = 0.064408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.049718 restraints weight = 107074.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.051019 restraints weight = 52477.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.051805 restraints weight = 33865.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.052233 restraints weight = 25860.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.052379 restraints weight = 22130.020| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11963 Z= 0.164 Angle : 0.636 11.656 17123 Z= 0.361 Chirality : 0.040 0.270 2021 Planarity : 0.003 0.027 1458 Dihedral : 30.764 178.665 3422 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.58 % Allowed : 34.76 % Favored : 59.67 % 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: 0.71 (0.27), residues: 974 helix: 1.18 (0.24), residues: 475 sheet: 0.90 (0.43), residues: 145 loop : -0.61 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 67 TYR 0.011 0.001 TYR F 51 PHE 0.014 0.001 PHE E 84 TRP 0.000 0.000 TRP K 690 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00358 (11963) covalent geometry : angle 0.63586 (17123) hydrogen bonds : bond 0.06278 ( 669) hydrogen bonds : angle 3.61465 ( 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 192 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.339 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: G 70 LEU cc_start: 0.9667 (tp) cc_final: 0.9098 (mt) REVERT: G 73 GLU cc_start: 0.8051 (tt0) cc_final: 0.7447 (mt-10) REVERT: G 84 PHE cc_start: 0.8699 (m-10) cc_final: 0.8004 (m-80) REVERT: G 120 MET cc_start: 0.9064 (mmt) cc_final: 0.8823 (mmm) REVERT: H 39 ARG cc_start: 0.8924 (mmm-85) cc_final: 0.8386 (mmm-85) REVERT: H 44 LYS cc_start: 0.9431 (tppt) cc_final: 0.8943 (tppt) REVERT: H 88 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: E 64 LYS cc_start: 0.9621 (mmmm) cc_final: 0.9278 (mmmm) REVERT: E 68 GLN cc_start: 0.9674 (tt0) cc_final: 0.9340 (tp40) REVERT: E 90 MET cc_start: 0.9464 (tpp) cc_final: 0.9196 (tpp) REVERT: F 84 MET cc_start: 0.9175 (tpp) cc_final: 0.8527 (tpp) REVERT: F 88 TYR cc_start: 0.9389 (m-80) cc_final: 0.8764 (m-80) REVERT: C 94 GLU cc_start: 0.8870 (tp30) cc_final: 0.8191 (tp30) REVERT: C 97 GLU cc_start: 0.8169 (pp20) cc_final: 0.7892 (pp20) REVERT: C 120 MET cc_start: 0.9339 (mtp) cc_final: 0.9097 (mmm) REVERT: D 25 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8153 (p0) REVERT: D 26 ILE cc_start: 0.9660 (OUTLIER) cc_final: 0.9351 (tp) REVERT: D 53 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8821 (tm-30) REVERT: D 91 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8457 (mmtm) REVERT: A 78 PHE cc_start: 0.9373 (t80) cc_final: 0.9075 (t80) REVERT: A 90 MET cc_start: 0.9034 (mtm) cc_final: 0.8744 (mmm) REVERT: A 94 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8571 (mm-30) REVERT: A 97 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8999 (pp20) REVERT: A 129 ARG cc_start: 0.9777 (ptm160) cc_final: 0.9546 (ptm-80) REVERT: B 53 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8697 (mm-30) REVERT: B 64 ASN cc_start: 0.9599 (m-40) cc_final: 0.9357 (p0) outliers start: 30 outliers final: 15 residues processed: 183 average time/residue: 0.1163 time to fit residues: 29.2816 Evaluate side-chains 165 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG 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 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 125 GLN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 114 optimal weight: 50.0000 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.0270 chunk 66 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 50.0000 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 40.0000 overall best weight: 3.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.061571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046828 restraints weight = 109317.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.048065 restraints weight = 53878.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.048730 restraints weight = 34974.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.049278 restraints weight = 27187.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.049508 restraints weight = 22910.344| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11963 Z= 0.229 Angle : 0.677 11.855 17123 Z= 0.382 Chirality : 0.041 0.199 2021 Planarity : 0.004 0.038 1458 Dihedral : 31.107 178.384 3422 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 7.06 % Allowed : 34.39 % Favored : 58.55 % 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: 0.78 (0.27), residues: 974 helix: 1.23 (0.24), residues: 475 sheet: 0.97 (0.44), residues: 141 loop : -0.57 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 67 TYR 0.019 0.002 TYR E 54 PHE 0.012 0.001 PHE E 84 TRP 0.000 0.000 TRP K 690 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00503 (11963) covalent geometry : angle 0.67701 (17123) hydrogen bonds : bond 0.06801 ( 669) hydrogen bonds : angle 3.78759 ( 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 191 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.236 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: 0.9674 (tp) cc_final: 0.9101 (mt) REVERT: G 73 GLU cc_start: 0.8091 (tt0) cc_final: 0.7424 (mt-10) REVERT: G 84 PHE cc_start: 0.8791 (m-10) cc_final: 0.8343 (m-10) REVERT: H 39 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8466 (mmm-85) REVERT: H 44 LYS cc_start: 0.9270 (tppt) cc_final: 0.8910 (tppt) REVERT: H 88 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: E 64 LYS cc_start: 0.9620 (mmmm) cc_final: 0.9324 (mmmm) REVERT: E 84 PHE cc_start: 0.8728 (m-80) cc_final: 0.8514 (m-10) REVERT: E 97 GLU cc_start: 0.9238 (tp30) cc_final: 0.8967 (mm-30) REVERT: F 63 GLU cc_start: 0.8765 (tp30) cc_final: 0.8482 (tp30) REVERT: F 84 MET cc_start: 0.9181 (tpp) cc_final: 0.8591 (tpp) REVERT: F 88 TYR cc_start: 0.9468 (m-80) cc_final: 0.8964 (m-80) REVERT: C 54 TYR cc_start: 0.8982 (m-80) cc_final: 0.8627 (m-80) REVERT: C 94 GLU cc_start: 0.8964 (tp30) cc_final: 0.8244 (tp30) REVERT: C 97 GLU cc_start: 0.8227 (pp20) cc_final: 0.7940 (pp20) REVERT: C 105 GLU cc_start: 0.9423 (mm-30) cc_final: 0.8855 (mm-30) REVERT: C 120 MET cc_start: 0.9365 (mtp) cc_final: 0.8989 (mmm) REVERT: D 25 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8250 (p0) REVERT: D 26 ILE cc_start: 0.9703 (OUTLIER) cc_final: 0.9439 (tp) REVERT: D 53 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8855 (tm-30) REVERT: D 63 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9139 (mm-30) REVERT: D 91 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8552 (mmtm) REVERT: A 78 PHE cc_start: 0.9350 (t80) cc_final: 0.9073 (t80) REVERT: A 90 MET cc_start: 0.9080 (mtm) cc_final: 0.8726 (mmm) REVERT: A 94 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8581 (mm-30) REVERT: A 129 ARG cc_start: 0.9781 (ptm160) cc_final: 0.9496 (ptm-80) REVERT: B 52 GLU cc_start: 0.9314 (pm20) cc_final: 0.8938 (pm20) REVERT: B 53 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8833 (mm-30) REVERT: B 55 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8595 (mmm-85) outliers start: 38 outliers final: 20 residues processed: 183 average time/residue: 0.1111 time to fit residues: 28.2771 Evaluate side-chains 168 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG 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 96 CYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 117 VAL 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 125 GLN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 50.0000 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 40.0000 chunk 85 optimal weight: 7.9990 chunk 80 optimal weight: 40.0000 chunk 65 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 GLN ** 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 = 0.3648 r_free = 0.3648 target = 0.062137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.047559 restraints weight = 108945.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.048831 restraints weight = 53253.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.049600 restraints weight = 34226.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.049904 restraints weight = 26040.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.050272 restraints weight = 22938.584| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11963 Z= 0.187 Angle : 0.683 14.999 17123 Z= 0.379 Chirality : 0.040 0.234 2021 Planarity : 0.003 0.028 1458 Dihedral : 31.073 177.248 3422 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.58 % Allowed : 36.62 % Favored : 57.81 % 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: 0.80 (0.27), residues: 974 helix: 1.21 (0.24), residues: 475 sheet: 0.99 (0.44), residues: 141 loop : -0.50 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 35 TYR 0.010 0.001 TYR H 88 PHE 0.011 0.001 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00416 (11963) covalent geometry : angle 0.68254 (17123) hydrogen bonds : bond 0.06259 ( 669) hydrogen bonds : angle 3.66396 ( 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 183 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.269 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: G 63 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.9086 (tpm170) REVERT: G 73 GLU cc_start: 0.8079 (tt0) cc_final: 0.7424 (mt-10) REVERT: H 39 ARG cc_start: 0.8900 (mmm-85) cc_final: 0.8424 (mmm-85) REVERT: H 44 LYS cc_start: 0.9255 (tppt) cc_final: 0.8881 (tppt) REVERT: H 67 ARG cc_start: 0.9131 (ttm110) cc_final: 0.8764 (ttm110) REVERT: H 88 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: E 64 LYS cc_start: 0.9592 (mmmm) cc_final: 0.9342 (mmmm) REVERT: E 97 GLU cc_start: 0.9217 (tp30) cc_final: 0.8915 (mm-30) REVERT: F 63 GLU cc_start: 0.8814 (tp30) cc_final: 0.8530 (tp30) REVERT: F 84 MET cc_start: 0.9168 (tpp) cc_final: 0.8528 (tpp) REVERT: F 88 TYR cc_start: 0.9443 (m-80) cc_final: 0.8912 (m-80) REVERT: C 54 TYR cc_start: 0.8987 (m-80) cc_final: 0.8631 (m-80) REVERT: C 94 GLU cc_start: 0.8963 (tp30) cc_final: 0.8205 (tp30) REVERT: C 97 GLU cc_start: 0.8203 (pp20) cc_final: 0.7888 (pp20) REVERT: C 105 GLU cc_start: 0.9438 (mm-30) cc_final: 0.8818 (mm-30) REVERT: C 110 CYS cc_start: 0.9719 (m) cc_final: 0.9442 (m) REVERT: C 120 MET cc_start: 0.9317 (mtp) cc_final: 0.9104 (mmm) REVERT: D 25 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8165 (p0) REVERT: D 26 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9395 (tp) REVERT: D 52 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8824 (pp20) REVERT: D 53 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8849 (tm-30) REVERT: D 63 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9116 (mm-30) REVERT: D 91 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8543 (mmtm) REVERT: A 78 PHE cc_start: 0.9370 (t80) cc_final: 0.9044 (t80) REVERT: A 90 MET cc_start: 0.9116 (mtm) cc_final: 0.8712 (mmm) REVERT: A 94 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8646 (mm-30) REVERT: A 129 ARG cc_start: 0.9772 (ptm160) cc_final: 0.9474 (ptm-80) REVERT: B 52 GLU cc_start: 0.9280 (pm20) cc_final: 0.8986 (pm20) REVERT: B 53 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8801 (mm-30) outliers start: 30 outliers final: 22 residues processed: 177 average time/residue: 0.1155 time to fit residues: 28.0218 Evaluate side-chains 172 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL 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 29 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 112 optimal weight: 50.0000 chunk 79 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 0.0040 chunk 12 optimal weight: 5.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 GLN ** 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 = 0.3689 r_free = 0.3689 target = 0.065677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.050496 restraints weight = 109007.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.051804 restraints weight = 53666.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.052605 restraints weight = 34721.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.053021 restraints weight = 26551.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.053166 restraints weight = 22696.597| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11963 Z= 0.153 Angle : 0.672 13.450 17123 Z= 0.373 Chirality : 0.040 0.230 2021 Planarity : 0.003 0.031 1458 Dihedral : 30.867 177.866 3422 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.20 % Allowed : 37.36 % 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: 0.73 (0.27), residues: 974 helix: 1.17 (0.24), residues: 477 sheet: 0.88 (0.44), residues: 149 loop : -0.57 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 35 TYR 0.013 0.001 TYR E 54 PHE 0.013 0.001 PHE E 104 TRP 0.000 0.000 TRP K 690 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00331 (11963) covalent geometry : angle 0.67230 (17123) hydrogen bonds : bond 0.06261 ( 669) hydrogen bonds : angle 3.53401 ( 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 191 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.341 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 63 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.8586 (tpt170) REVERT: G 82 LEU cc_start: 0.8116 (mm) cc_final: 0.7838 (mm) REVERT: G 129 ARG cc_start: 0.9106 (ttp80) cc_final: 0.8881 (ttp-110) REVERT: H 39 ARG cc_start: 0.8840 (mmm-85) cc_final: 0.8273 (mmm-85) REVERT: H 44 LYS cc_start: 0.9163 (tppt) cc_final: 0.8727 (tppt) REVERT: H 88 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: E 64 LYS cc_start: 0.9588 (mmmm) cc_final: 0.9333 (mmmm) REVERT: E 97 GLU cc_start: 0.9065 (tp30) cc_final: 0.8830 (mm-30) REVERT: F 63 GLU cc_start: 0.8812 (tp30) cc_final: 0.8460 (tp30) REVERT: F 84 MET cc_start: 0.9108 (tpp) cc_final: 0.8400 (tpp) REVERT: F 88 TYR cc_start: 0.9428 (m-80) cc_final: 0.8921 (m-80) REVERT: C 94 GLU cc_start: 0.8935 (tp30) cc_final: 0.8109 (tp30) REVERT: C 97 GLU cc_start: 0.8249 (pp20) cc_final: 0.7889 (pp20) REVERT: C 119 ILE cc_start: 0.9455 (pt) cc_final: 0.9036 (mm) REVERT: D 25 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8067 (p0) REVERT: D 52 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8788 (pp20) REVERT: D 53 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8780 (tm-30) REVERT: A 78 PHE cc_start: 0.9414 (t80) cc_final: 0.9090 (t80) REVERT: A 90 MET cc_start: 0.9151 (mtm) cc_final: 0.8785 (mmm) REVERT: A 94 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8595 (mm-30) REVERT: A 129 ARG cc_start: 0.9767 (ptm160) cc_final: 0.9465 (ptm-80) REVERT: B 52 GLU cc_start: 0.9302 (pm20) cc_final: 0.8946 (pm20) REVERT: B 53 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8764 (mm-30) REVERT: B 55 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8733 (mtp85) outliers start: 28 outliers final: 17 residues processed: 182 average time/residue: 0.1194 time to fit residues: 29.6649 Evaluate side-chains 170 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 86 VAL 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 A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 75 HIS 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: 50.0000 chunk 56 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 111 optimal weight: 50.0000 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 125 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 = 0.3603 r_free = 0.3603 target = 0.059879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.045293 restraints weight = 109960.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.046525 restraints weight = 54613.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.047270 restraints weight = 35567.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.047667 restraints weight = 27389.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.048001 restraints weight = 23522.199| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11963 Z= 0.267 Angle : 0.754 14.313 17123 Z= 0.415 Chirality : 0.043 0.479 2021 Planarity : 0.005 0.115 1458 Dihedral : 31.303 178.104 3422 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.76 % Allowed : 37.36 % Favored : 56.88 % 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: 0.66 (0.27), residues: 974 helix: 0.93 (0.24), residues: 482 sheet: 1.06 (0.44), residues: 141 loop : -0.41 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 35 TYR 0.011 0.001 TYR H 88 PHE 0.043 0.002 PHE A 67 TRP 0.000 0.000 TRP K 690 HIS 0.006 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00588 (11963) covalent geometry : angle 0.75406 (17123) hydrogen bonds : bond 0.07190 ( 669) hydrogen bonds : angle 3.95024 ( 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 176 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.315 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: G 73 GLU cc_start: 0.8126 (tt0) cc_final: 0.7438 (mt-10) REVERT: G 129 ARG cc_start: 0.9223 (ttp80) cc_final: 0.8890 (ttp-110) REVERT: H 39 ARG cc_start: 0.8918 (mmm-85) cc_final: 0.8267 (mmm-85) REVERT: H 44 LYS cc_start: 0.9284 (tppt) cc_final: 0.8711 (tppt) REVERT: H 67 ARG cc_start: 0.9120 (ttm110) cc_final: 0.8778 (ttm110) REVERT: H 88 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8513 (m-80) REVERT: E 64 LYS cc_start: 0.9596 (mmmm) cc_final: 0.9346 (mmmm) REVERT: E 97 GLU cc_start: 0.9254 (tp30) cc_final: 0.8853 (mm-30) REVERT: F 63 GLU cc_start: 0.8831 (tp30) cc_final: 0.8427 (tp30) REVERT: F 84 MET cc_start: 0.9165 (tpp) cc_final: 0.8573 (tpp) REVERT: F 88 TYR cc_start: 0.9493 (m-80) cc_final: 0.9063 (m-80) REVERT: C 94 GLU cc_start: 0.9069 (tp30) cc_final: 0.8385 (tp30) REVERT: C 97 GLU cc_start: 0.8277 (pp20) cc_final: 0.7958 (pp20) REVERT: C 120 MET cc_start: 0.9316 (mmm) cc_final: 0.8730 (mmt) REVERT: D 25 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8550 (p0) REVERT: D 53 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8843 (tm-30) REVERT: A 78 PHE cc_start: 0.9390 (t80) cc_final: 0.9053 (t80) REVERT: A 90 MET cc_start: 0.9178 (mtm) cc_final: 0.8789 (mmm) REVERT: A 94 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8703 (mm-30) REVERT: A 129 ARG cc_start: 0.9785 (ptm160) cc_final: 0.9485 (ptm-80) REVERT: B 52 GLU cc_start: 0.9253 (pm20) cc_final: 0.8850 (pm20) REVERT: B 53 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8946 (mm-30) REVERT: B 55 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.8997 (mtt180) outliers start: 31 outliers final: 22 residues processed: 170 average time/residue: 0.1184 time to fit residues: 27.7987 Evaluate side-chains 162 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 37 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 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 75 HIS 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: 6.9990 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 50.0000 chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 104 optimal weight: 50.0000 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 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 = 0.3616 r_free = 0.3616 target = 0.062045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.046729 restraints weight = 113260.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.048011 restraints weight = 55749.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.048768 restraints weight = 36252.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.049264 restraints weight = 27950.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.049484 restraints weight = 23825.996| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.5043 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= 0.213 Angle : 0.738 14.762 17123 Z= 0.404 Chirality : 0.042 0.421 2021 Planarity : 0.005 0.090 1458 Dihedral : 31.295 177.329 3422 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.83 % Allowed : 37.92 % Favored : 57.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.27), residues: 974 helix: 0.91 (0.24), residues: 477 sheet: 0.86 (0.44), residues: 144 loop : -0.44 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 67 TYR 0.009 0.001 TYR H 88 PHE 0.012 0.002 PHE G 84 TRP 0.000 0.000 TRP K 690 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00469 (11963) covalent geometry : angle 0.73848 (17123) hydrogen bonds : bond 0.06390 ( 669) hydrogen bonds : angle 3.86671 ( 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 167 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 GLU cc_start: 0.8105 (tt0) cc_final: 0.7623 (mp0) REVERT: G 129 ARG cc_start: 0.9189 (ttp80) cc_final: 0.8954 (ttp-110) REVERT: H 39 ARG cc_start: 0.8944 (mmm-85) cc_final: 0.8421 (mmm-85) REVERT: H 44 LYS cc_start: 0.9290 (tppt) cc_final: 0.8824 (tppt) REVERT: H 67 ARG cc_start: 0.9116 (ttm110) cc_final: 0.8760 (ttm110) REVERT: H 88 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: E 64 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9287 (mmmm) REVERT: E 90 MET cc_start: 0.9412 (tpp) cc_final: 0.9180 (tpp) REVERT: E 97 GLU cc_start: 0.9166 (tp30) cc_final: 0.8785 (mm-30) REVERT: F 63 GLU cc_start: 0.8799 (tp30) cc_final: 0.8408 (tp30) REVERT: F 84 MET cc_start: 0.9149 (tpp) cc_final: 0.8526 (tpp) REVERT: F 88 TYR cc_start: 0.9475 (m-80) cc_final: 0.9025 (m-80) REVERT: C 94 GLU cc_start: 0.9045 (tp30) cc_final: 0.8333 (tp30) REVERT: C 97 GLU cc_start: 0.8238 (pp20) cc_final: 0.7923 (pp20) REVERT: C 110 CYS cc_start: 0.9715 (m) cc_final: 0.9416 (m) REVERT: C 120 MET cc_start: 0.9345 (mmm) cc_final: 0.9025 (mmt) REVERT: D 25 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8297 (p0) REVERT: D 53 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8740 (tm-30) REVERT: A 78 PHE cc_start: 0.9422 (t80) cc_final: 0.9110 (t80) REVERT: A 90 MET cc_start: 0.9178 (mtm) cc_final: 0.8784 (mmm) REVERT: A 94 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8710 (mm-30) REVERT: A 129 ARG cc_start: 0.9770 (ptm160) cc_final: 0.9462 (ptm-80) REVERT: B 52 GLU cc_start: 0.9272 (pm20) cc_final: 0.8882 (pm20) REVERT: B 53 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8962 (mm-30) REVERT: B 55 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.9035 (mtt180) outliers start: 26 outliers final: 21 residues processed: 162 average time/residue: 0.1158 time to fit residues: 26.0554 Evaluate side-chains 163 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 126 LEU 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 96 CYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 37 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 25 ASN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 75 HIS 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: 0.8980 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.0970 chunk 115 optimal weight: 9.9990 chunk 104 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 17 optimal weight: 7.9990 overall best weight: 2.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 55 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 = 0.3618 r_free = 0.3618 target = 0.062176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.046910 restraints weight = 112946.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.048214 restraints weight = 55817.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.048640 restraints weight = 36261.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.049377 restraints weight = 29641.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.049641 restraints weight = 24509.458| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11963 Z= 0.200 Angle : 0.752 14.442 17123 Z= 0.409 Chirality : 0.043 0.417 2021 Planarity : 0.005 0.086 1458 Dihedral : 31.274 177.693 3422 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.65 % Allowed : 38.66 % Favored : 56.69 % 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: 0.51 (0.27), residues: 974 helix: 0.84 (0.23), residues: 479 sheet: 0.93 (0.44), residues: 146 loop : -0.49 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 67 TYR 0.022 0.001 TYR C 54 PHE 0.037 0.002 PHE A 67 TRP 0.000 0.000 TRP K 690 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00443 (11963) covalent geometry : angle 0.75221 (17123) hydrogen bonds : bond 0.06353 ( 669) hydrogen bonds : angle 3.92426 ( 1689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.32 seconds wall clock time: 41 minutes 51.25 seconds (2511.25 seconds total)