Starting phenix.real_space_refine on Fri Jul 3 06:34:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y60_33630/07_2026/7y60_33630.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y60_33630/07_2026/7y60_33630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y60_33630/07_2026/7y60_33630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y60_33630/07_2026/7y60_33630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y60_33630/07_2026/7y60_33630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y60_33630/07_2026/7y60_33630.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1848 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 216 5.49 5 S 20 5.16 5 C 6418 2.51 5 N 2172 2.21 5 O 2552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11378 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 761 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "F" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 591 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2198 Classifications: {'DNA': 108} Link IDs: {'rna3p': 107} Chain: "C" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 732 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "D" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 583 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "J" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2230 Classifications: {'DNA': 108} Link IDs: {'rna3p': 107} Chain: "K" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 99 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "L" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 1749 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 13, 'TRANS': 340} Chain breaks: 4 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1113 Unresolved non-hydrogen angles: 1439 Unresolved non-hydrogen dihedrals: 949 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLU:plan': 14, 'TRP:plan': 8, 'HIS:plan': 10, 'ASN:plan1': 15, 'TYR:plan': 13, 'ASP:plan': 22, 'PHE:plan': 17, 'GLN:plan1': 7, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 600 Time building chain proxies: 2.41, per 1000 atoms: 0.21 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: 0.83 Conformation dependent library (CDL) restraints added in 264.2 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: 1.14 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: 1.80 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2326 1.33 - 1.45: 3591 1.45 - 1.58: 5584 1.58 - 1.70: 430 1.70 - 1.82: 32 Bond restraints: 11963 Sorted by residual: bond pdb=" C3' DG I 25 " pdb=" C2' DG I 25 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" C3' DG J 124 " pdb=" C2' DG J 124 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DG J 69 " pdb=" C2' DG J 69 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG I 102 " pdb=" C2' DG I 102 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA I 60 " pdb=" C2' DA I 60 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 11958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 16748 2.30 - 4.59: 341 4.59 - 6.89: 27 6.89 - 9.18: 6 9.18 - 11.48: 1 Bond angle restraints: 17123 Sorted by residual: angle pdb=" C LEU G 65 " pdb=" N PRO G 66 " pdb=" CA PRO G 66 " ideal model delta sigma weight residual 118.85 127.59 -8.74 1.09e+00 8.42e-01 6.44e+01 angle pdb=" N LYS G 64 " pdb=" CA LYS G 64 " pdb=" C LYS G 64 " ideal model delta sigma weight residual 111.28 119.29 -8.01 1.09e+00 8.42e-01 5.40e+01 angle pdb=" CA LEU G 65 " pdb=" C LEU G 65 " pdb=" N PRO G 66 " ideal model delta sigma weight residual 120.93 116.13 4.80 1.06e+00 8.90e-01 2.05e+01 angle pdb=" N3 DT I 46 " pdb=" C4 DT I 46 " pdb=" O4 DT I 46 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" O4' DA I 65 " pdb=" C4' DA I 65 " pdb=" C3' DA I 65 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.99e+01 ... (remaining 17118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 5462 35.09 - 70.17: 1123 70.17 - 105.26: 37 105.26 - 140.34: 0 140.34 - 175.43: 4 Dihedral angle restraints: 6626 sinusoidal: 3721 harmonic: 2905 Sorted by residual: dihedral pdb=" CA PHE K 711 " pdb=" C PHE K 711 " pdb=" N LEU K 712 " pdb=" CA LEU K 712 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" C4' DC I 82 " pdb=" C3' DC I 82 " pdb=" O3' DC I 82 " pdb=" P DG I 83 " ideal model delta sinusoidal sigma weight residual 220.00 44.57 175.43 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC I 79 " pdb=" C3' DC I 79 " pdb=" O3' DC I 79 " pdb=" P DC I 80 " ideal model delta sinusoidal sigma weight residual -140.00 33.97 -173.97 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1497 0.049 - 0.097: 432 0.097 - 0.146: 87 0.146 - 0.194: 4 0.194 - 0.243: 1 Chirality restraints: 2021 Sorted by residual: chirality pdb=" CA LYS G 64 " pdb=" N LYS G 64 " pdb=" C LYS G 64 " pdb=" CB LYS G 64 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C3' DC I 79 " pdb=" C4' DC I 79 " pdb=" O3' DC I 79 " pdb=" C2' DC I 79 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" C3' DC I 82 " pdb=" C4' DC I 82 " pdb=" O3' DC I 82 " pdb=" C2' DC I 82 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 2018 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 63 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ARG G 63 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG G 63 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS G 64 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 82 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C LEU G 82 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU G 82 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG G 83 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU G 65 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO G 66 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 66 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 66 " -0.021 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1111 2.74 - 3.28: 10944 3.28 - 3.82: 21860 3.82 - 4.36: 23489 4.36 - 4.90: 34819 Nonbonded interactions: 92223 Sorted by model distance: nonbonded pdb=" O2 DC I 56 " pdb=" N2 DG J 92 " model vdw 2.200 2.496 nonbonded pdb=" N2 DG I 37 " pdb=" O2 DC J 111 " model vdw 2.219 2.496 nonbonded pdb=" O2 DC I 54 " pdb=" N2 DG J 94 " model vdw 2.231 2.496 nonbonded pdb=" N2 DG I 67 " pdb=" O2 DC J 81 " model vdw 2.239 2.496 nonbonded pdb=" OG1 THR E 118 " pdb=" NH1 ARG F 45 " model vdw 2.240 3.120 ... (remaining 92218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 59 through 134) selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 26 through 97) selection = (chain 'D' and resid 26 through 97) selection = (chain 'F' and resid 26 through 97) selection = (chain 'H' and resid 26 through 97) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 10.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11963 Z= 0.460 Angle : 0.792 11.477 17123 Z= 0.643 Chirality : 0.046 0.243 2021 Planarity : 0.004 0.048 1458 Dihedral : 28.445 175.426 4730 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.30 % Allowed : 34.39 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 974 helix: 0.66 (0.24), residues: 461 sheet: 0.40 (0.45), residues: 132 loop : -1.04 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 40 TYR 0.019 0.001 TYR C 99 PHE 0.022 0.001 PHE G 84 TRP 0.000 0.000 TRP K 690 HIS 0.009 0.003 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.46 (11963) covalent geometry : angle 0.79187 / 0.64 (17123) hydrogen bonds : bond 0.14707 / 9.81 ( 669) hydrogen bonds : angle 5.61335 / 3.88 ( 1689) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 236 time to evaluate : 0.249 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: 0.1214 time to fit residues: 38.7795 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 : 0.226 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 20.0000 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: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3711 r_free = 0.3711 target = 0.067961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.052254 restraints weight = 108814.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.053622 restraints weight = 52968.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.054409 restraints weight = 34367.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.054973 restraints weight = 26631.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.055200 restraints weight = 22598.066| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1919 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= 0.193 Angle : 0.744 8.125 17123 Z= 0.423 Chirality : 0.050 0.321 2021 Planarity : 0.005 0.064 1458 Dihedral : 30.855 177.247 3422 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.20 % Allowed : 32.90 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 974 helix: 0.58 (0.23), residues: 471 sheet: 0.34 (0.43), residues: 135 loop : -1.01 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 92 TYR 0.015 0.001 TYR F 88 PHE 0.018 0.002 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.008 0.003 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 (11963) covalent geometry : angle 0.74399 / 0.42 (17123) hydrogen bonds : bond 0.07827 / 5.24 ( 669) hydrogen bonds : angle 4.37809 / 3.05 ( 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 206 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 GLU cc_start: 0.7794 (tt0) cc_final: 0.7253 (mt-10) REVERT: H 88 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: E 64 LYS cc_start: 0.9552 (mmmm) cc_final: 0.9252 (mmmm) REVERT: E 90 MET cc_start: 0.9516 (tpp) cc_final: 0.9227 (mmp) REVERT: F 84 MET cc_start: 0.9204 (tpp) cc_final: 0.8537 (tpp) REVERT: F 88 TYR cc_start: 0.9484 (m-10) cc_final: 0.8884 (m-80) REVERT: C 74 ILE cc_start: 0.9755 (tt) cc_final: 0.9456 (tt) REVERT: C 94 GLU cc_start: 0.9189 (tp30) cc_final: 0.8303 (tp30) REVERT: D 25 ASN cc_start: 0.8986 (OUTLIER) cc_final: 0.8546 (p0) REVERT: D 63 GLU cc_start: 0.8995 (tp30) cc_final: 0.8778 (mm-30) REVERT: D 77 LYS cc_start: 0.9639 (tptp) cc_final: 0.9392 (tppt) REVERT: D 85 ASP cc_start: 0.8943 (m-30) cc_final: 0.8616 (t0) REVERT: A 90 MET cc_start: 0.8933 (mtm) cc_final: 0.8484 (mtm) REVERT: A 128 ARG cc_start: 0.9269 (mmm-85) cc_final: 0.8704 (mmm-85) REVERT: A 133 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8165 (mp0) REVERT: B 29 ILE cc_start: 0.8986 (mm) cc_final: 0.8784 (mp) outliers start: 28 outliers final: 15 residues processed: 196 average time/residue: 0.1023 time to fit residues: 27.6473 Evaluate side-chains 175 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain B residue 31 LYS 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: 50.0000 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3695 r_free = 0.3695 target = 0.065296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.050396 restraints weight = 107650.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.051716 restraints weight = 52664.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.052501 restraints weight = 34108.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.052946 restraints weight = 26139.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.053321 restraints weight = 22402.086| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11963 Z= 0.193 Angle : 0.704 8.430 17123 Z= 0.403 Chirality : 0.047 0.298 2021 Planarity : 0.004 0.059 1458 Dihedral : 30.963 179.093 3422 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.13 % Allowed : 31.60 % Favored : 62.27 % 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: -0.00 (0.26), residues: 974 helix: 0.70 (0.23), residues: 470 sheet: 0.33 (0.43), residues: 137 loop : -0.97 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 134 TYR 0.010 0.001 TYR C 99 PHE 0.017 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/Z covalent geometry : bond 0.00363 / 0.19 (11963) covalent geometry : angle 0.70424 / 0.40 (17123) hydrogen bonds : bond 0.07453 / 5.02 ( 669) hydrogen bonds : angle 4.12794 / 2.89 ( 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 198 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 GLU cc_start: 0.7851 (tt0) cc_final: 0.7318 (mt-10) REVERT: H 88 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: E 64 LYS cc_start: 0.9574 (mmmm) cc_final: 0.9315 (mmmm) REVERT: E 120 MET cc_start: 0.9186 (mmm) cc_final: 0.8966 (mmm) REVERT: F 84 MET cc_start: 0.9270 (tpp) cc_final: 0.8665 (tpp) REVERT: F 88 TYR cc_start: 0.9466 (m-10) cc_final: 0.9012 (m-80) REVERT: C 74 ILE cc_start: 0.9758 (tt) cc_final: 0.9473 (tt) REVERT: C 94 GLU cc_start: 0.8950 (tp30) cc_final: 0.8464 (tp30) REVERT: D 25 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8236 (p0) REVERT: D 53 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8731 (tm-30) REVERT: D 77 LYS cc_start: 0.9650 (tptp) cc_final: 0.9421 (tppt) REVERT: D 85 ASP cc_start: 0.8953 (m-30) cc_final: 0.8651 (t0) REVERT: D 91 LYS cc_start: 0.9243 (tptt) cc_final: 0.8789 (mmtm) REVERT: A 90 MET cc_start: 0.8976 (mtm) cc_final: 0.8769 (mmm) REVERT: A 92 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9407 (pp) REVERT: A 94 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8634 (mm-30) outliers start: 33 outliers final: 20 residues processed: 188 average time/residue: 0.0941 time to fit residues: 24.9072 Evaluate side-chains 177 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 89 VAL 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 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 70 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 89 optimal weight: 50.0000 chunk 79 optimal weight: 50.0000 chunk 105 optimal weight: 40.0000 chunk 100 optimal weight: 50.0000 chunk 28 optimal weight: 8.9990 overall best weight: 3.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.065741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.049983 restraints weight = 110788.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.051314 restraints weight = 54355.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.052130 restraints weight = 35391.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.052529 restraints weight = 27195.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.052935 restraints weight = 23497.150| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11963 Z= 0.206 Angle : 0.702 8.188 17123 Z= 0.402 Chirality : 0.047 0.286 2021 Planarity : 0.004 0.037 1458 Dihedral : 31.078 178.059 3422 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.76 % Allowed : 32.16 % 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: 0.16 (0.26), residues: 974 helix: 0.78 (0.24), residues: 474 sheet: 0.39 (0.44), residues: 137 loop : -0.80 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 128 TYR 0.009 0.001 TYR C 99 PHE 0.018 0.002 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.007 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.21 (11963) covalent geometry : angle 0.70153 / 0.40 (17123) hydrogen bonds : bond 0.07547 / 5.09 ( 669) hydrogen bonds : angle 4.09368 / 2.87 ( 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 198 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.250 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: 0.9689 (tp) cc_final: 0.9148 (mt) REVERT: G 73 GLU cc_start: 0.7867 (tt0) cc_final: 0.7583 (mt-10) REVERT: H 88 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: E 64 LYS cc_start: 0.9584 (mmmm) cc_final: 0.9316 (mmmm) REVERT: E 105 GLU cc_start: 0.9207 (tp30) cc_final: 0.8923 (mm-30) REVERT: E 118 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8807 (m) REVERT: E 120 MET cc_start: 0.9235 (mmm) cc_final: 0.8943 (mmm) REVERT: F 84 MET cc_start: 0.9226 (tpp) cc_final: 0.8736 (tpp) REVERT: F 88 TYR cc_start: 0.9469 (m-10) cc_final: 0.9073 (m-80) REVERT: C 94 GLU cc_start: 0.9047 (tp30) cc_final: 0.8449 (mm-30) REVERT: C 97 GLU cc_start: 0.8314 (pp20) cc_final: 0.7926 (pp20) REVERT: C 105 GLU cc_start: 0.9277 (mm-30) cc_final: 0.9050 (mm-30) REVERT: D 53 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8753 (tm-30) REVERT: D 77 LYS cc_start: 0.9677 (tptp) cc_final: 0.9470 (tppt) REVERT: D 91 LYS cc_start: 0.9265 (tptt) cc_final: 0.8991 (mmtt) REVERT: A 78 PHE cc_start: 0.8748 (m-10) cc_final: 0.8183 (m-10) REVERT: A 90 MET cc_start: 0.8946 (mtm) cc_final: 0.8277 (mtm) REVERT: A 94 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8642 (mm-30) REVERT: A 120 MET cc_start: 0.8291 (mmt) cc_final: 0.7877 (mmm) REVERT: A 133 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8169 (mp0) REVERT: B 52 GLU cc_start: 0.9364 (pm20) cc_final: 0.9161 (pm20) REVERT: B 53 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8795 (mm-30) REVERT: B 63 GLU cc_start: 0.9372 (tm-30) cc_final: 0.9004 (tm-30) outliers start: 31 outliers final: 21 residues processed: 189 average time/residue: 0.0942 time to fit residues: 24.9886 Evaluate side-chains 175 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 chunk 19 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 27 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.066582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.051001 restraints weight = 109663.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.052357 restraints weight = 53566.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.053176 restraints weight = 34748.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.053607 restraints weight = 26591.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.053996 restraints weight = 22798.293| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11963 Z= 0.152 Angle : 0.690 8.891 17123 Z= 0.391 Chirality : 0.047 0.272 2021 Planarity : 0.004 0.037 1458 Dihedral : 31.089 176.267 3422 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.39 % Allowed : 34.01 % Favored : 60.59 % 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: 0.26 (0.26), residues: 974 helix: 0.82 (0.24), residues: 475 sheet: 0.48 (0.44), residues: 137 loop : -0.71 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 134 TYR 0.011 0.001 TYR C 99 PHE 0.014 0.002 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.008 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (11963) covalent geometry : angle 0.69049 / 0.39 (17123) hydrogen bonds : bond 0.06813 / 4.57 ( 669) hydrogen bonds : angle 3.91631 / 2.75 ( 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 200 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 LEU cc_start: 0.9684 (tp) cc_final: 0.9134 (mt) REVERT: G 73 GLU cc_start: 0.8145 (tt0) cc_final: 0.7547 (mt-10) REVERT: G 84 PHE cc_start: 0.8712 (m-10) cc_final: 0.8314 (m-10) REVERT: H 88 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8486 (m-80) REVERT: E 54 TYR cc_start: 0.8348 (m-10) cc_final: 0.8107 (m-10) REVERT: E 64 LYS cc_start: 0.9591 (mmmm) cc_final: 0.9297 (mmmm) REVERT: E 68 GLN cc_start: 0.9714 (tt0) cc_final: 0.9272 (tp40) REVERT: E 105 GLU cc_start: 0.9195 (tp30) cc_final: 0.8913 (mm-30) REVERT: E 120 MET cc_start: 0.9272 (mmm) cc_final: 0.9029 (mmm) REVERT: F 63 GLU cc_start: 0.8906 (tp30) cc_final: 0.8684 (tp30) REVERT: F 84 MET cc_start: 0.9161 (tpp) cc_final: 0.8560 (tpp) REVERT: F 88 TYR cc_start: 0.9421 (m-10) cc_final: 0.8930 (m-80) REVERT: C 94 GLU cc_start: 0.9003 (tp30) cc_final: 0.8464 (tp30) REVERT: C 105 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9036 (mm-30) REVERT: D 53 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8673 (tm-30) REVERT: D 77 LYS cc_start: 0.9658 (tptp) cc_final: 0.9450 (tppt) REVERT: D 84 MET cc_start: 0.8817 (tpp) cc_final: 0.8596 (tmm) REVERT: D 85 ASP cc_start: 0.8894 (m-30) cc_final: 0.8580 (t0) REVERT: D 91 LYS cc_start: 0.9235 (tptt) cc_final: 0.8699 (mmtm) REVERT: A 90 MET cc_start: 0.8937 (mtm) cc_final: 0.8647 (mmm) REVERT: A 94 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8623 (mm-30) REVERT: A 97 GLU cc_start: 0.9251 (tm-30) cc_final: 0.9036 (pp20) REVERT: A 120 MET cc_start: 0.8265 (mmt) cc_final: 0.7786 (mmm) REVERT: B 52 GLU cc_start: 0.9344 (pm20) cc_final: 0.9098 (pm20) REVERT: B 53 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8814 (mm-30) REVERT: B 67 ARG cc_start: 0.9623 (tpp80) cc_final: 0.9352 (tpp80) outliers start: 29 outliers final: 19 residues processed: 190 average time/residue: 0.0972 time to fit residues: 25.5235 Evaluate side-chains 174 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU 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 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 26 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 114 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 81 optimal weight: 40.0000 chunk 69 optimal weight: 30.0000 chunk 80 optimal weight: 40.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS A 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.049026 restraints weight = 107634.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.050301 restraints weight = 52813.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.051093 restraints weight = 34145.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.051490 restraints weight = 26181.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.051868 restraints weight = 22475.743| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11963 Z= 0.181 Angle : 0.714 9.372 17123 Z= 0.401 Chirality : 0.047 0.345 2021 Planarity : 0.004 0.051 1458 Dihedral : 31.106 177.119 3422 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.02 % Allowed : 34.94 % 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: 0.29 (0.27), residues: 974 helix: 0.81 (0.24), residues: 475 sheet: 0.52 (0.44), residues: 137 loop : -0.66 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 45 TYR 0.011 0.001 TYR C 99 PHE 0.030 0.002 PHE A 67 TRP 0.000 0.000 TRP K 690 HIS 0.006 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 (11963) covalent geometry : angle 0.71395 / 0.40 (17123) hydrogen bonds : bond 0.07133 / 4.82 ( 669) hydrogen bonds : angle 3.92544 / 2.76 ( 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 185 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 LEU cc_start: 0.9670 (tp) cc_final: 0.9116 (mt) REVERT: G 73 GLU cc_start: 0.8096 (tt0) cc_final: 0.7541 (mt-10) REVERT: G 84 PHE cc_start: 0.8720 (m-10) cc_final: 0.8336 (m-10) REVERT: G 120 MET cc_start: 0.9056 (mmt) cc_final: 0.8783 (mmm) REVERT: G 125 GLN cc_start: 0.9449 (mt0) cc_final: 0.9135 (mm-40) REVERT: H 88 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8505 (m-80) REVERT: E 64 LYS cc_start: 0.9620 (mmmm) cc_final: 0.9374 (mmmm) REVERT: E 68 GLN cc_start: 0.9704 (tt0) cc_final: 0.9337 (tp40) REVERT: E 105 GLU cc_start: 0.9207 (tp30) cc_final: 0.8919 (mm-30) REVERT: E 120 MET cc_start: 0.9248 (mmm) cc_final: 0.9023 (mmm) REVERT: F 84 MET cc_start: 0.9167 (tpp) cc_final: 0.8609 (tpp) REVERT: F 88 TYR cc_start: 0.9412 (m-10) cc_final: 0.9024 (m-80) REVERT: D 53 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8758 (tm-30) REVERT: D 60 VAL cc_start: 0.9731 (t) cc_final: 0.9527 (p) REVERT: D 77 LYS cc_start: 0.9679 (tptp) cc_final: 0.9471 (tppt) REVERT: D 84 MET cc_start: 0.8827 (tpp) cc_final: 0.8574 (tmm) REVERT: D 85 ASP cc_start: 0.8884 (m-30) cc_final: 0.8561 (t0) REVERT: D 91 LYS cc_start: 0.9254 (tptt) cc_final: 0.8994 (tppt) REVERT: A 78 PHE cc_start: 0.8376 (m-80) cc_final: 0.8001 (m-80) REVERT: A 92 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9389 (pp) REVERT: A 94 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8562 (mm-30) REVERT: A 120 MET cc_start: 0.8324 (mmt) cc_final: 0.7846 (mmm) REVERT: A 133 GLU cc_start: 0.8360 (mp0) cc_final: 0.8134 (mp0) REVERT: B 67 ARG cc_start: 0.9619 (tpp80) cc_final: 0.9300 (tpp80) outliers start: 27 outliers final: 20 residues processed: 176 average time/residue: 0.1112 time to fit residues: 27.4455 Evaluate side-chains 174 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 85 optimal weight: 50.0000 chunk 80 optimal weight: 50.0000 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.053789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.036852 restraints weight = 86085.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.037961 restraints weight = 47765.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.038699 restraints weight = 33097.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.039159 restraints weight = 26266.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.039451 restraints weight = 22838.646| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11963 Z= 0.151 Angle : 0.709 16.609 17123 Z= 0.396 Chirality : 0.047 0.257 2021 Planarity : 0.004 0.038 1458 Dihedral : 31.114 176.006 3422 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.28 % Allowed : 35.13 % Favored : 60.59 % 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: 0.32 (0.27), residues: 974 helix: 0.81 (0.24), residues: 475 sheet: 0.55 (0.43), residues: 144 loop : -0.64 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.013 0.001 TYR E 54 PHE 0.014 0.001 PHE E 67 TRP 0.000 0.000 TRP K 690 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (11963) covalent geometry : angle 0.70904 / 0.40 (17123) hydrogen bonds : bond 0.06695 / 4.48 ( 669) hydrogen bonds : angle 3.82929 / 2.69 ( 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 187 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.283 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: 0.9650 (tp) cc_final: 0.9072 (mt) REVERT: G 73 GLU cc_start: 0.8080 (tt0) cc_final: 0.7524 (mt-10) REVERT: G 84 PHE cc_start: 0.8717 (m-10) cc_final: 0.8341 (m-10) REVERT: G 120 MET cc_start: 0.9075 (mmt) cc_final: 0.8869 (mmm) REVERT: G 125 GLN cc_start: 0.9466 (mt0) cc_final: 0.9139 (mm-40) REVERT: H 88 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: E 54 TYR cc_start: 0.8519 (m-10) cc_final: 0.8186 (m-10) REVERT: E 64 LYS cc_start: 0.9629 (mmmm) cc_final: 0.9268 (mmmm) REVERT: E 68 GLN cc_start: 0.9691 (tt0) cc_final: 0.9334 (tp40) REVERT: E 105 GLU cc_start: 0.9215 (tp30) cc_final: 0.8922 (mm-30) REVERT: E 120 MET cc_start: 0.9270 (mmm) cc_final: 0.9033 (mmm) REVERT: F 63 GLU cc_start: 0.8920 (tp30) cc_final: 0.8718 (tp30) REVERT: F 84 MET cc_start: 0.9167 (tpp) cc_final: 0.8489 (tpp) REVERT: F 88 TYR cc_start: 0.9397 (m-10) cc_final: 0.8851 (m-80) REVERT: C 94 GLU cc_start: 0.8970 (tp30) cc_final: 0.8719 (tp30) REVERT: C 105 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9175 (mm-30) REVERT: D 53 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8673 (tm-30) REVERT: D 60 VAL cc_start: 0.9728 (t) cc_final: 0.9500 (p) REVERT: D 77 LYS cc_start: 0.9658 (tptp) cc_final: 0.9410 (tppt) REVERT: D 84 MET cc_start: 0.8827 (tpp) cc_final: 0.8583 (tmm) REVERT: D 85 ASP cc_start: 0.8900 (m-30) cc_final: 0.8586 (t0) REVERT: A 78 PHE cc_start: 0.8310 (m-10) cc_final: 0.7349 (m-80) REVERT: A 94 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8636 (mm-30) REVERT: A 97 GLU cc_start: 0.9252 (tm-30) cc_final: 0.9022 (pp20) REVERT: A 120 MET cc_start: 0.8358 (mmt) cc_final: 0.7890 (mmm) REVERT: B 52 GLU cc_start: 0.9369 (pm20) cc_final: 0.9041 (pm20) REVERT: B 53 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8882 (mm-30) REVERT: B 67 ARG cc_start: 0.9671 (tpp80) cc_final: 0.9424 (tpp80) outliers start: 23 outliers final: 15 residues processed: 181 average time/residue: 0.1059 time to fit residues: 26.9377 Evaluate side-chains 172 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 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 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER 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: 0.8980 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 35 optimal weight: 20.0000 chunk 112 optimal weight: 40.0000 chunk 79 optimal weight: 50.0000 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.054451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.037584 restraints weight = 85859.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.038765 restraints weight = 46885.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.039498 restraints weight = 32493.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.039975 restraints weight = 25792.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.040154 restraints weight = 22293.713| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11963 Z= 0.145 Angle : 0.710 16.901 17123 Z= 0.394 Chirality : 0.047 0.249 2021 Planarity : 0.004 0.055 1458 Dihedral : 31.049 176.020 3422 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.72 % Allowed : 36.99 % Favored : 59.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.26), residues: 974 helix: 0.70 (0.23), residues: 475 sheet: 0.65 (0.43), residues: 145 loop : -0.69 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 134 TYR 0.011 0.001 TYR C 99 PHE 0.017 0.002 PHE A 67 TRP 0.000 0.000 TRP K 690 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (11963) covalent geometry : angle 0.71044 / 0.39 (17123) hydrogen bonds : bond 0.06706 / 4.46 ( 669) hydrogen bonds : angle 3.82612 / 2.70 ( 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 182 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 LEU cc_start: 0.9622 (tp) cc_final: 0.9152 (tp) REVERT: G 73 GLU cc_start: 0.8070 (tt0) cc_final: 0.7496 (mt-10) REVERT: G 84 PHE cc_start: 0.8685 (m-10) cc_final: 0.8256 (m-10) REVERT: H 88 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: E 64 LYS cc_start: 0.9621 (mmmm) cc_final: 0.9272 (mmmm) REVERT: E 68 GLN cc_start: 0.9687 (tt0) cc_final: 0.9336 (tp40) REVERT: E 105 GLU cc_start: 0.9194 (tp30) cc_final: 0.8901 (mm-30) REVERT: E 120 MET cc_start: 0.9252 (mmm) cc_final: 0.8993 (mmm) REVERT: F 84 MET cc_start: 0.9170 (tpp) cc_final: 0.8467 (tpp) REVERT: F 88 TYR cc_start: 0.9390 (m-10) cc_final: 0.8846 (m-80) REVERT: C 105 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9170 (mm-30) REVERT: D 53 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8680 (tm-30) REVERT: D 60 VAL cc_start: 0.9700 (t) cc_final: 0.9496 (p) REVERT: D 77 LYS cc_start: 0.9639 (tptp) cc_final: 0.9383 (tppt) REVERT: D 84 MET cc_start: 0.8870 (tpp) cc_final: 0.8615 (tmm) REVERT: D 85 ASP cc_start: 0.8882 (m-30) cc_final: 0.8600 (t0) REVERT: D 91 LYS cc_start: 0.9038 (mmtm) cc_final: 0.8550 (mmtm) REVERT: A 78 PHE cc_start: 0.8273 (m-10) cc_final: 0.7259 (m-80) REVERT: A 90 MET cc_start: 0.8909 (mtm) cc_final: 0.8595 (mtt) REVERT: A 94 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8607 (mm-30) REVERT: A 97 GLU cc_start: 0.9240 (tm-30) cc_final: 0.9025 (pp20) REVERT: A 120 MET cc_start: 0.8357 (mmt) cc_final: 0.7878 (mmm) REVERT: A 128 ARG cc_start: 0.9365 (mmm-85) cc_final: 0.9109 (mmm-85) REVERT: B 67 ARG cc_start: 0.9689 (tpp80) cc_final: 0.9437 (tpp80) outliers start: 20 outliers final: 14 residues processed: 178 average time/residue: 0.1178 time to fit residues: 28.8934 Evaluate side-chains 169 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 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: 5.9990 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 111 optimal weight: 50.0000 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.063431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.048589 restraints weight = 106780.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.049854 restraints weight = 52608.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.050588 restraints weight = 34256.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.051104 restraints weight = 26492.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.051331 restraints weight = 22510.933| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11963 Z= 0.189 Angle : 0.736 16.986 17123 Z= 0.407 Chirality : 0.046 0.248 2021 Planarity : 0.004 0.084 1458 Dihedral : 31.120 177.320 3422 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.53 % Allowed : 38.29 % Favored : 58.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.27), residues: 974 helix: 0.76 (0.24), residues: 475 sheet: 0.58 (0.43), residues: 147 loop : -0.74 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 134 TYR 0.011 0.001 TYR C 99 PHE 0.021 0.002 PHE E 84 TRP 0.000 0.000 TRP K 690 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (11963) covalent geometry : angle 0.73623 / 0.41 (17123) hydrogen bonds : bond 0.07030 / 4.72 ( 669) hydrogen bonds : angle 3.90146 / 2.73 ( 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 177 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.321 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: 0.9625 (tp) cc_final: 0.9148 (tp) REVERT: G 73 GLU cc_start: 0.8077 (tt0) cc_final: 0.7503 (mt-10) REVERT: G 84 PHE cc_start: 0.8764 (m-10) cc_final: 0.8343 (m-10) REVERT: H 44 LYS cc_start: 0.9473 (tppp) cc_final: 0.8978 (tppt) REVERT: H 88 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: E 54 TYR cc_start: 0.8420 (m-10) cc_final: 0.8136 (m-10) REVERT: E 64 LYS cc_start: 0.9605 (mmmm) cc_final: 0.9282 (mmmm) REVERT: E 68 GLN cc_start: 0.9696 (tt0) cc_final: 0.9359 (tp40) REVERT: E 105 GLU cc_start: 0.9194 (tp30) cc_final: 0.8956 (mm-30) REVERT: E 120 MET cc_start: 0.9249 (mmm) cc_final: 0.8990 (mmm) REVERT: F 84 MET cc_start: 0.9168 (tpp) cc_final: 0.8578 (tpp) REVERT: F 88 TYR cc_start: 0.9381 (m-10) cc_final: 0.8949 (m-80) REVERT: C 105 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9174 (mm-30) REVERT: D 53 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8727 (tm-30) REVERT: D 77 LYS cc_start: 0.9674 (tptp) cc_final: 0.9468 (tppt) REVERT: D 91 LYS cc_start: 0.9085 (mmtm) cc_final: 0.8693 (mmtm) REVERT: A 78 PHE cc_start: 0.8331 (m-10) cc_final: 0.7303 (m-80) REVERT: A 90 MET cc_start: 0.8988 (mtm) cc_final: 0.8695 (mtt) REVERT: A 94 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8610 (mm-30) REVERT: A 97 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8965 (pp20) REVERT: A 120 MET cc_start: 0.8380 (mmt) cc_final: 0.7842 (mmm) REVERT: A 128 ARG cc_start: 0.9387 (mmm-85) cc_final: 0.9080 (mmm-85) REVERT: B 67 ARG cc_start: 0.9663 (tpp80) cc_final: 0.9406 (tpp80) outliers start: 19 outliers final: 15 residues processed: 174 average time/residue: 0.1126 time to fit residues: 27.2860 Evaluate side-chains 169 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 126 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 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 21 optimal weight: 0.0370 chunk 43 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 30.0000 chunk 2 optimal weight: 0.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.052204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035275 restraints weight = 89589.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036383 restraints weight = 50043.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.037069 restraints weight = 35199.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.037493 restraints weight = 28228.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.037660 restraints weight = 24674.051| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11963 Z= 0.201 Angle : 0.764 19.945 17123 Z= 0.418 Chirality : 0.047 0.244 2021 Planarity : 0.004 0.077 1458 Dihedral : 31.275 176.517 3422 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.97 % Allowed : 38.10 % Favored : 58.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.27), residues: 974 helix: 0.72 (0.23), residues: 475 sheet: 0.66 (0.43), residues: 143 loop : -0.73 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 134 TYR 0.013 0.001 TYR D 72 PHE 0.040 0.002 PHE A 67 TRP 0.000 0.000 TRP K 690 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.20 (11963) covalent geometry : angle 0.76449 / 0.42 (17123) hydrogen bonds : bond 0.07158 / 4.80 ( 669) hydrogen bonds : angle 4.00102 / 2.79 ( 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 172 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.342 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 73 GLU cc_start: 0.8112 (tt0) cc_final: 0.7554 (mt-10) REVERT: G 84 PHE cc_start: 0.8832 (m-10) cc_final: 0.8419 (m-10) REVERT: G 120 MET cc_start: 0.9164 (mmt) cc_final: 0.8963 (mmm) REVERT: H 44 LYS cc_start: 0.9514 (tppp) cc_final: 0.9087 (tptp) REVERT: H 59 LYS cc_start: 0.9641 (tppt) cc_final: 0.9407 (mmtt) REVERT: H 88 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8485 (m-80) REVERT: E 54 TYR cc_start: 0.8522 (m-10) cc_final: 0.8235 (m-10) REVERT: E 64 LYS cc_start: 0.9625 (mmmm) cc_final: 0.9309 (mmmm) REVERT: E 105 GLU cc_start: 0.9249 (tp30) cc_final: 0.8990 (mm-30) REVERT: E 120 MET cc_start: 0.9255 (mmm) cc_final: 0.8995 (mmm) REVERT: F 84 MET cc_start: 0.9241 (tpp) cc_final: 0.8631 (tpp) REVERT: F 88 TYR cc_start: 0.9431 (m-10) cc_final: 0.9062 (m-80) REVERT: C 94 GLU cc_start: 0.9038 (tp30) cc_final: 0.8827 (tp30) REVERT: C 105 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9234 (mm-30) REVERT: D 53 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8758 (tm-30) REVERT: D 77 LYS cc_start: 0.9683 (tptp) cc_final: 0.9453 (tppt) REVERT: D 91 LYS cc_start: 0.9132 (mmtm) cc_final: 0.8855 (mmtt) REVERT: A 78 PHE cc_start: 0.8294 (m-10) cc_final: 0.7229 (m-80) REVERT: A 90 MET cc_start: 0.8995 (mtm) cc_final: 0.8711 (mtt) REVERT: A 94 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8664 (mm-30) REVERT: A 97 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8963 (pp20) REVERT: A 120 MET cc_start: 0.8455 (mmt) cc_final: 0.7978 (mmm) REVERT: A 128 ARG cc_start: 0.9409 (mmm-85) cc_final: 0.9112 (mmm-85) REVERT: B 67 ARG cc_start: 0.9683 (tpp80) cc_final: 0.9420 (tpp80) outliers start: 16 outliers final: 14 residues processed: 168 average time/residue: 0.1144 time to fit residues: 26.8158 Evaluate side-chains 164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 TYR Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 126 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 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 30.0000 chunk 44 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 100 optimal weight: 50.0000 chunk 17 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.064526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.049176 restraints weight = 110464.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.050185 restraints weight = 54978.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.050890 restraints weight = 35662.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.051474 restraints weight = 27421.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.051672 restraints weight = 23414.128| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11963 Z= 0.165 Angle : 0.748 17.435 17123 Z= 0.411 Chirality : 0.047 0.235 2021 Planarity : 0.004 0.072 1458 Dihedral : 31.277 175.366 3422 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.97 % Allowed : 37.73 % Favored : 59.29 % 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: 0.27 (0.27), residues: 974 helix: 0.70 (0.23), residues: 477 sheet: 0.70 (0.43), residues: 147 loop : -0.65 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 134 TYR 0.009 0.001 TYR C 99 PHE 0.042 0.002 PHE A 67 TRP 0.000 0.000 TRP K 690 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (11963) covalent geometry : angle 0.74828 / 0.41 (17123) hydrogen bonds : bond 0.06718 / 4.51 ( 669) hydrogen bonds : angle 3.95053 / 2.78 ( 1689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2160.62 seconds wall clock time: 37 minutes 47.39 seconds (2267.39 seconds total)