Starting phenix.real_space_refine on Fri Jul 3 06:23:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txv_41706/07_2026/8txv_41706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txv_41706/07_2026/8txv_41706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8txv_41706/07_2026/8txv_41706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txv_41706/07_2026/8txv_41706.map" model { file = "/net/cci-nas-00/data/ceres_data/8txv_41706/07_2026/8txv_41706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txv_41706/07_2026/8txv_41706.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 15 5.16 5 C 7144 2.51 5 N 2407 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12836 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 117 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 2.89, per 1000 atoms: 0.23 Number of scatterers: 12836 At special positions: 0 Unit cell: (94.288, 124.832, 120.848, 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 15 16.00 P 294 15.00 O 2976 8.00 N 2407 7.00 C 7144 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 394.4 milliseconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 66.7% alpha, 4.4% beta 135 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.527A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.576A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.010A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.596A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.567A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.881A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.793A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.523A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.601A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) 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: 4.014A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.504A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.629A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.615A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.712A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 56 through 60 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.640A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.825A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.603A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.528A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.709A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB1, first strand: chain 'M' and resid 12 through 16 removed outlier: 8.825A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2529 1.33 - 1.45: 4339 1.45 - 1.57: 6179 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13659 Sorted by residual: bond pdb=" C3' DA J -68 " pdb=" C2' DA J -68 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DC I 33 " pdb=" C2' DC I 33 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DG I -41 " pdb=" C2' DG I -41 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT I 15 " pdb=" C2' DT I 15 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 ... (remaining 13654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 18390 1.44 - 2.87: 1226 2.87 - 4.31: 63 4.31 - 5.74: 14 5.74 - 7.18: 5 Bond angle restraints: 19698 Sorted by residual: angle pdb=" O4' DG I 26 " pdb=" C4' DG I 26 " pdb=" C3' DG I 26 " ideal model delta sigma weight residual 106.00 103.07 2.93 6.00e-01 2.78e+00 2.38e+01 angle pdb=" O4' DC I -18 " pdb=" C4' DC I -18 " pdb=" C3' DC I -18 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N3 DT I -28 " pdb=" C4 DT I -28 " pdb=" O4 DT I -28 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I -59 " pdb=" C4 DT I -59 " pdb=" O4 DT I -59 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT I 3 " pdb=" C4 DT I 3 " pdb=" O4 DT I 3 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 ... (remaining 19693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.37: 5861 29.37 - 58.74: 1527 58.74 - 88.12: 105 88.12 - 117.49: 2 117.49 - 146.86: 2 Dihedral angle restraints: 7497 sinusoidal: 5012 harmonic: 2485 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 73.14 146.86 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 75.89 144.11 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CB GLU C 56 " pdb=" CG GLU C 56 " pdb=" CD GLU C 56 " pdb=" OE1 GLU C 56 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1158 0.028 - 0.055: 644 0.055 - 0.083: 257 0.083 - 0.110: 158 0.110 - 0.138: 23 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE C 111 " pdb=" N ILE C 111 " pdb=" C ILE C 111 " pdb=" CB ILE C 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 2237 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.021 2.00e-02 2.50e+03 8.92e-03 2.19e+00 pdb=" N9 DA I -35 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.021 2.00e-02 2.50e+03 8.33e-03 2.08e+00 pdb=" N9 DG I 47 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.018 2.00e-02 2.50e+03 7.34e-03 1.61e+00 pdb=" N9 DG I 26 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " -0.001 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 493 2.70 - 3.25: 11464 3.25 - 3.80: 23895 3.80 - 4.35: 28492 4.35 - 4.90: 41650 Nonbonded interactions: 105994 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.151 2.496 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.219 3.040 nonbonded pdb=" NH2 ARG F 35 " pdb=" OP2 DC I 8 " model vdw 2.263 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.271 3.040 nonbonded pdb=" NH2 ARG D 31 " pdb=" OP1 DG J 51 " model vdw 2.297 3.120 ... (remaining 105989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.25 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.080 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 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 0.049 13661 Z= 0.492 Angle : 0.715 7.178 19704 Z= 0.630 Chirality : 0.043 0.138 2240 Planarity : 0.003 0.038 1478 Dihedral : 26.649 146.860 5891 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.30), residues: 839 helix: 2.61 (0.22), residues: 544 sheet: 1.56 (1.19), residues: 26 loop : -0.45 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 67 TYR 0.020 0.001 TYR H 40 PHE 0.009 0.001 PHE E 78 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.49 (13659) covalent geometry : angle 0.71541 / 0.63 (19698) hydrogen bonds : bond 0.10334 / 7.20 ( 768) hydrogen bonds : angle 3.99937 / 2.97 ( 1920) link_TRANS : bond 0.00080 / 0.04 ( 2) link_TRANS : angle 0.53035 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8391 (m-30) cc_final: 0.7864 (t70) REVERT: B 31 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8769 (ttpp) REVERT: B 91 LYS cc_start: 0.9420 (ttmm) cc_final: 0.9160 (ttmt) REVERT: D 51 ASP cc_start: 0.9279 (p0) cc_final: 0.8711 (p0) REVERT: D 116 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8989 (ttmt) REVERT: D 120 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8735 (tttt) REVERT: E 57 SER cc_start: 0.9388 (p) cc_final: 0.8894 (p) REVERT: E 59 GLU cc_start: 0.8782 (pm20) cc_final: 0.7941 (pm20) REVERT: E 82 LEU cc_start: 0.9341 (mt) cc_final: 0.9119 (mm) REVERT: E 94 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8359 (mm-30) REVERT: E 110 CYS cc_start: 0.7930 (m) cc_final: 0.7655 (m) REVERT: E 129 ARG cc_start: 0.8949 (tpt90) cc_final: 0.8744 (tpt-90) REVERT: F 91 LYS cc_start: 0.9101 (tttp) cc_final: 0.8743 (ttmt) REVERT: H 59 MET cc_start: 0.8960 (tpt) cc_final: 0.8643 (tpp) REVERT: H 85 LYS cc_start: 0.9341 (mttm) cc_final: 0.8926 (mttp) REVERT: C 64 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8415 (tm-30) REVERT: G 41 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8418 (tm-30) REVERT: G 64 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8684 (tm-30) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1321 time to fit residues: 40.9475 Evaluate side-chains 179 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.088547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.056770 restraints weight = 53175.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.059127 restraints weight = 22362.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.060650 restraints weight = 13793.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.061633 restraints weight = 10568.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.062119 restraints weight = 9115.866| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (11 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13661 Z= 0.158 Angle : 0.615 6.430 19704 Z= 0.375 Chirality : 0.042 0.221 2240 Planarity : 0.004 0.036 1478 Dihedral : 29.865 151.724 4171 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.66 % Allowed : 11.51 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.29), residues: 839 helix: 2.57 (0.22), residues: 554 sheet: 1.11 (1.15), residues: 26 loop : -0.53 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.013 0.002 TYR H 83 PHE 0.011 0.001 PHE A 78 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.16 (13659) covalent geometry : angle 0.61527 / 0.38 (19698) hydrogen bonds : bond 0.05294 / 3.52 ( 768) hydrogen bonds : angle 3.34111 / 2.50 ( 1920) link_TRANS : bond 0.00072 / 0.04 ( 2) link_TRANS : angle 0.48775 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8107 (tt0) cc_final: 0.7552 (tt0) REVERT: A 81 ASP cc_start: 0.8188 (m-30) cc_final: 0.7921 (t70) REVERT: A 125 GLN cc_start: 0.8210 (mt0) cc_final: 0.7694 (mp10) REVERT: B 25 ASN cc_start: 0.8656 (m-40) cc_final: 0.8052 (m110) REVERT: B 31 LYS cc_start: 0.9182 (ttmt) cc_final: 0.8977 (ttpp) REVERT: B 91 LYS cc_start: 0.9444 (ttmm) cc_final: 0.9138 (ttmt) REVERT: D 51 ASP cc_start: 0.9035 (p0) cc_final: 0.8369 (p0) REVERT: D 85 LYS cc_start: 0.9358 (mttm) cc_final: 0.9024 (mmtt) REVERT: E 57 SER cc_start: 0.9311 (p) cc_final: 0.8782 (p) REVERT: E 59 GLU cc_start: 0.8759 (pm20) cc_final: 0.7943 (pm20) REVERT: F 85 ASP cc_start: 0.8703 (m-30) cc_final: 0.8129 (m-30) REVERT: F 91 LYS cc_start: 0.9278 (tttp) cc_final: 0.8999 (ttmt) REVERT: H 83 TYR cc_start: 0.8570 (m-10) cc_final: 0.8304 (m-10) REVERT: H 85 LYS cc_start: 0.9320 (mttm) cc_final: 0.8855 (mtmm) REVERT: M 61 ILE cc_start: 0.2575 (tp) cc_final: 0.2043 (mm) REVERT: C 64 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8448 (tm-30) REVERT: G 41 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8087 (tm-30) REVERT: G 64 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8748 (tm-30) outliers start: 11 outliers final: 9 residues processed: 189 average time/residue: 0.1264 time to fit residues: 32.7772 Evaluate side-chains 181 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.086783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.054650 restraints weight = 61463.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.057030 restraints weight = 24084.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.058570 restraints weight = 14441.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.059574 restraints weight = 10878.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.060094 restraints weight = 9285.318| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13661 Z= 0.191 Angle : 0.641 8.481 19704 Z= 0.376 Chirality : 0.042 0.217 2240 Planarity : 0.004 0.037 1478 Dihedral : 30.063 154.179 4171 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.91 % Allowed : 13.04 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.29), residues: 839 helix: 2.63 (0.22), residues: 554 sheet: 1.32 (1.05), residues: 26 loop : -0.65 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG M 42 TYR 0.024 0.002 TYR D 42 PHE 0.016 0.001 PHE A 78 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (13659) covalent geometry : angle 0.64124 / 0.38 (19698) hydrogen bonds : bond 0.05277 / 3.53 ( 768) hydrogen bonds : angle 3.31989 / 2.48 ( 1920) link_TRANS : bond 0.00106 / 0.05 ( 2) link_TRANS : angle 0.32287 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8158 (tt0) cc_final: 0.7553 (tt0) REVERT: A 81 ASP cc_start: 0.8173 (m-30) cc_final: 0.7916 (t70) REVERT: A 125 GLN cc_start: 0.8199 (mt0) cc_final: 0.7347 (mp10) REVERT: A 129 ARG cc_start: 0.8924 (tpt90) cc_final: 0.8471 (tpt90) REVERT: B 25 ASN cc_start: 0.8659 (m-40) cc_final: 0.8025 (m110) REVERT: B 88 TYR cc_start: 0.8506 (m-10) cc_final: 0.7926 (m-10) REVERT: B 91 LYS cc_start: 0.9469 (ttmm) cc_final: 0.9183 (ttmt) REVERT: D 46 LYS cc_start: 0.9465 (tppt) cc_final: 0.9185 (tppt) REVERT: D 51 ASP cc_start: 0.9077 (p0) cc_final: 0.8517 (p0) REVERT: D 83 TYR cc_start: 0.8144 (m-10) cc_final: 0.7750 (m-10) REVERT: D 85 LYS cc_start: 0.9385 (mttm) cc_final: 0.9123 (mmtt) REVERT: E 57 SER cc_start: 0.9389 (p) cc_final: 0.8836 (p) REVERT: E 59 GLU cc_start: 0.8793 (pm20) cc_final: 0.8056 (pm20) REVERT: F 88 TYR cc_start: 0.8396 (m-10) cc_final: 0.7750 (m-10) REVERT: F 91 LYS cc_start: 0.9326 (tttp) cc_final: 0.8973 (ttmt) REVERT: H 85 LYS cc_start: 0.9321 (mttm) cc_final: 0.8927 (mttp) REVERT: C 64 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8477 (tm-30) REVERT: G 41 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8051 (tm-30) outliers start: 20 outliers final: 17 residues processed: 192 average time/residue: 0.1274 time to fit residues: 33.1573 Evaluate side-chains 192 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.052711 restraints weight = 52308.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.054890 restraints weight = 22904.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.056303 restraints weight = 14472.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.057172 restraints weight = 11202.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.057718 restraints weight = 9770.310| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 13661 Z= 0.274 Angle : 0.713 8.368 19704 Z= 0.404 Chirality : 0.045 0.231 2240 Planarity : 0.005 0.059 1478 Dihedral : 30.252 155.966 4171 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.47 % Allowed : 16.09 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.29), residues: 839 helix: 2.40 (0.22), residues: 554 sheet: 1.46 (1.23), residues: 18 loop : -0.76 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 72 TYR 0.022 0.002 TYR B 88 PHE 0.010 0.002 PHE A 78 HIS 0.007 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.27 (13659) covalent geometry : angle 0.71322 / 0.40 (19698) hydrogen bonds : bond 0.05935 / 3.96 ( 768) hydrogen bonds : angle 3.57360 / 2.66 ( 1920) link_TRANS : bond 0.00243 / 0.12 ( 2) link_TRANS : angle 0.37374 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8116 (m-30) cc_final: 0.7915 (t70) REVERT: A 125 GLN cc_start: 0.8233 (mt0) cc_final: 0.7377 (mp10) REVERT: B 25 ASN cc_start: 0.8657 (m-40) cc_final: 0.8054 (m110) REVERT: B 91 LYS cc_start: 0.9480 (ttmm) cc_final: 0.9168 (ttmt) REVERT: D 46 LYS cc_start: 0.9491 (tppt) cc_final: 0.9269 (tppt) REVERT: D 51 ASP cc_start: 0.9087 (p0) cc_final: 0.8576 (p0) REVERT: D 85 LYS cc_start: 0.9388 (mttm) cc_final: 0.9166 (mmtt) REVERT: E 57 SER cc_start: 0.9338 (p) cc_final: 0.8942 (p) REVERT: E 59 GLU cc_start: 0.8810 (pm20) cc_final: 0.8147 (pm20) REVERT: F 91 LYS cc_start: 0.9388 (tttp) cc_final: 0.9030 (ttmt) REVERT: H 85 LYS cc_start: 0.9311 (mttm) cc_final: 0.8910 (mttp) REVERT: C 64 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8486 (tm-30) REVERT: G 41 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8008 (tm-30) outliers start: 24 outliers final: 21 residues processed: 183 average time/residue: 0.1191 time to fit residues: 30.6165 Evaluate side-chains 187 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 0.0470 chunk 98 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.055884 restraints weight = 42991.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.058045 restraints weight = 19897.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.059426 restraints weight = 12886.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.060212 restraints weight = 10137.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.060725 restraints weight = 8936.974| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13661 Z= 0.151 Angle : 0.610 8.570 19704 Z= 0.364 Chirality : 0.041 0.217 2240 Planarity : 0.004 0.043 1478 Dihedral : 30.094 154.507 4171 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.05 % Allowed : 17.48 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.30), residues: 839 helix: 2.66 (0.22), residues: 554 sheet: 1.13 (1.03), residues: 26 loop : -0.64 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.023 0.002 TYR B 88 PHE 0.012 0.001 PHE E 78 HIS 0.005 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (13659) covalent geometry : angle 0.60978 / 0.36 (19698) hydrogen bonds : bond 0.04923 / 3.28 ( 768) hydrogen bonds : angle 3.08899 / 2.30 ( 1920) link_TRANS : bond 0.00040 / 0.02 ( 2) link_TRANS : angle 0.39623 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8173 (mt0) cc_final: 0.7292 (mt0) REVERT: B 25 ASN cc_start: 0.8568 (m-40) cc_final: 0.7907 (m110) REVERT: B 88 TYR cc_start: 0.8370 (m-10) cc_final: 0.8126 (m-10) REVERT: B 91 LYS cc_start: 0.9460 (ttmm) cc_final: 0.9122 (ttmt) REVERT: D 46 LYS cc_start: 0.9454 (tppt) cc_final: 0.9242 (tppt) REVERT: D 51 ASP cc_start: 0.9008 (p0) cc_final: 0.8477 (p0) REVERT: D 85 LYS cc_start: 0.9377 (mttm) cc_final: 0.9176 (mmtt) REVERT: E 57 SER cc_start: 0.9360 (p) cc_final: 0.8977 (p) REVERT: E 59 GLU cc_start: 0.8761 (pm20) cc_final: 0.8112 (pm20) REVERT: F 91 LYS cc_start: 0.9328 (tttp) cc_final: 0.8979 (ttmt) REVERT: H 85 LYS cc_start: 0.9307 (mttm) cc_final: 0.8852 (mtmm) REVERT: C 64 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8562 (tm-30) REVERT: G 41 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7960 (tm-30) outliers start: 21 outliers final: 19 residues processed: 191 average time/residue: 0.1143 time to fit residues: 30.6615 Evaluate side-chains 189 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN M 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.054204 restraints weight = 46043.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.056350 restraints weight = 20844.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.057714 restraints weight = 13434.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.058457 restraints weight = 10541.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.059013 restraints weight = 9307.728| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13661 Z= 0.214 Angle : 0.664 9.393 19704 Z= 0.383 Chirality : 0.042 0.222 2240 Planarity : 0.004 0.037 1478 Dihedral : 30.210 156.064 4171 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.19 % Allowed : 19.00 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.29), residues: 839 helix: 2.57 (0.22), residues: 554 sheet: 1.65 (1.25), residues: 18 loop : -0.82 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 42 TYR 0.036 0.002 TYR B 88 PHE 0.008 0.001 PHE E 78 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (13659) covalent geometry : angle 0.66392 / 0.38 (19698) hydrogen bonds : bond 0.05295 / 3.53 ( 768) hydrogen bonds : angle 3.27041 / 2.43 ( 1920) link_TRANS : bond 0.00136 / 0.07 ( 2) link_TRANS : angle 0.29377 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8230 (mt0) cc_final: 0.7375 (mt0) REVERT: B 25 ASN cc_start: 0.8619 (m-40) cc_final: 0.7965 (m110) REVERT: B 91 LYS cc_start: 0.9474 (ttmm) cc_final: 0.9165 (ttmt) REVERT: D 34 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8869 (mmmm) REVERT: D 46 LYS cc_start: 0.9461 (tppt) cc_final: 0.9185 (tppt) REVERT: D 51 ASP cc_start: 0.9041 (p0) cc_final: 0.8524 (p0) REVERT: D 83 TYR cc_start: 0.8295 (m-10) cc_final: 0.7874 (m-10) REVERT: D 85 LYS cc_start: 0.9387 (mttm) cc_final: 0.9185 (mmtt) REVERT: E 57 SER cc_start: 0.9347 (p) cc_final: 0.8837 (p) REVERT: E 59 GLU cc_start: 0.8760 (pm20) cc_final: 0.8010 (pm20) REVERT: F 91 LYS cc_start: 0.9355 (tttp) cc_final: 0.9007 (ttmt) REVERT: H 83 TYR cc_start: 0.8521 (m-10) cc_final: 0.8318 (m-10) REVERT: H 85 LYS cc_start: 0.9294 (mttm) cc_final: 0.8881 (mttp) REVERT: C 64 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8454 (tm-30) REVERT: G 41 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8011 (tm-30) outliers start: 22 outliers final: 19 residues processed: 178 average time/residue: 0.1242 time to fit residues: 30.8083 Evaluate side-chains 182 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.054560 restraints weight = 48231.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.056760 restraints weight = 21230.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.058160 restraints weight = 13467.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.059023 restraints weight = 10470.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.059540 restraints weight = 9158.076| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13661 Z= 0.185 Angle : 0.642 8.931 19704 Z= 0.374 Chirality : 0.041 0.218 2240 Planarity : 0.004 0.037 1478 Dihedral : 30.197 156.347 4171 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.88 % Allowed : 18.17 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.29), residues: 839 helix: 2.62 (0.22), residues: 554 sheet: 1.23 (1.06), residues: 26 loop : -0.82 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 33 TYR 0.032 0.002 TYR B 88 PHE 0.010 0.001 PHE E 78 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (13659) covalent geometry : angle 0.64220 / 0.37 (19698) hydrogen bonds : bond 0.05107 / 3.40 ( 768) hydrogen bonds : angle 3.14724 / 2.34 ( 1920) link_TRANS : bond 0.00092 / 0.04 ( 2) link_TRANS : angle 0.32418 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9210 (m-30) cc_final: 0.8920 (m-30) REVERT: A 125 GLN cc_start: 0.8233 (mt0) cc_final: 0.7455 (mt0) REVERT: B 25 ASN cc_start: 0.8606 (m-40) cc_final: 0.7940 (m110) REVERT: B 91 LYS cc_start: 0.9476 (ttmm) cc_final: 0.9181 (ttmt) REVERT: D 34 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8892 (mmmm) REVERT: D 51 ASP cc_start: 0.9020 (p0) cc_final: 0.8545 (p0) REVERT: D 83 TYR cc_start: 0.7931 (m-10) cc_final: 0.7731 (m-10) REVERT: D 85 LYS cc_start: 0.9383 (mttm) cc_final: 0.9180 (mmtt) REVERT: E 57 SER cc_start: 0.9329 (p) cc_final: 0.8801 (p) REVERT: E 59 GLU cc_start: 0.8735 (pm20) cc_final: 0.8054 (pm20) REVERT: F 88 TYR cc_start: 0.8572 (m-10) cc_final: 0.7489 (m-10) REVERT: F 91 LYS cc_start: 0.9355 (tttp) cc_final: 0.9009 (ttmt) REVERT: H 83 TYR cc_start: 0.8416 (m-10) cc_final: 0.8124 (m-10) REVERT: H 85 LYS cc_start: 0.9284 (mttm) cc_final: 0.8881 (mttp) REVERT: C 64 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8475 (tm-30) REVERT: G 41 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8025 (tm-30) outliers start: 27 outliers final: 23 residues processed: 182 average time/residue: 0.1174 time to fit residues: 30.1682 Evaluate side-chains 187 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 91 optimal weight: 0.4980 chunk 84 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.086652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.054616 restraints weight = 60989.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.057000 restraints weight = 24065.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.058551 restraints weight = 14467.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.059529 restraints weight = 10902.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.060052 restraints weight = 9372.542| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13661 Z= 0.157 Angle : 0.625 8.968 19704 Z= 0.367 Chirality : 0.041 0.214 2240 Planarity : 0.004 0.037 1478 Dihedral : 30.172 156.455 4171 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.74 % Allowed : 18.86 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.30), residues: 839 helix: 2.70 (0.22), residues: 553 sheet: 1.26 (1.06), residues: 26 loop : -0.75 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 42 TYR 0.020 0.002 TYR D 83 PHE 0.010 0.001 PHE E 78 HIS 0.005 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (13659) covalent geometry : angle 0.62518 / 0.37 (19698) hydrogen bonds : bond 0.04914 / 3.27 ( 768) hydrogen bonds : angle 3.06658 / 2.29 ( 1920) link_TRANS : bond 0.00039 / 0.02 ( 2) link_TRANS : angle 0.34623 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9218 (m-30) cc_final: 0.8927 (m-30) REVERT: A 125 GLN cc_start: 0.8226 (mt0) cc_final: 0.7421 (mt0) REVERT: B 25 ASN cc_start: 0.8580 (m-40) cc_final: 0.7846 (m110) REVERT: B 67 ARG cc_start: 0.7518 (mmp80) cc_final: 0.6943 (tpp80) REVERT: B 91 LYS cc_start: 0.9452 (ttmm) cc_final: 0.9153 (ttmt) REVERT: D 51 ASP cc_start: 0.9023 (p0) cc_final: 0.8468 (p0) REVERT: E 57 SER cc_start: 0.9332 (p) cc_final: 0.8771 (p) REVERT: E 59 GLU cc_start: 0.8712 (pm20) cc_final: 0.8051 (pm20) REVERT: F 88 TYR cc_start: 0.8625 (m-10) cc_final: 0.7509 (m-10) REVERT: F 91 LYS cc_start: 0.9338 (tttp) cc_final: 0.9081 (ttmt) REVERT: H 83 TYR cc_start: 0.8425 (m-10) cc_final: 0.8153 (m-10) REVERT: H 85 LYS cc_start: 0.9317 (mttm) cc_final: 0.8917 (mttp) REVERT: C 64 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8461 (tm-30) REVERT: G 41 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8022 (tm-30) outliers start: 26 outliers final: 21 residues processed: 181 average time/residue: 0.1124 time to fit residues: 28.9611 Evaluate side-chains 186 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 84 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN M 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.056634 restraints weight = 39288.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.058697 restraints weight = 18839.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.060030 restraints weight = 12527.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.060731 restraints weight = 10000.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.061235 restraints weight = 8912.953| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13661 Z= 0.148 Angle : 0.622 8.648 19704 Z= 0.365 Chirality : 0.040 0.206 2240 Planarity : 0.004 0.037 1478 Dihedral : 30.124 156.699 4171 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.33 % Allowed : 19.14 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.29), residues: 839 helix: 2.74 (0.22), residues: 554 sheet: 1.09 (1.04), residues: 26 loop : -0.69 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 42 TYR 0.016 0.001 TYR H 83 PHE 0.010 0.001 PHE E 78 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (13659) covalent geometry : angle 0.62158 / 0.37 (19698) hydrogen bonds : bond 0.04666 / 3.10 ( 768) hydrogen bonds : angle 2.97149 / 2.22 ( 1920) link_TRANS : bond 0.00039 / 0.02 ( 2) link_TRANS : angle 0.39528 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9215 (m-30) cc_final: 0.8898 (m-30) REVERT: A 125 GLN cc_start: 0.8207 (mt0) cc_final: 0.7386 (mt0) REVERT: B 25 ASN cc_start: 0.8564 (m-40) cc_final: 0.7775 (m110) REVERT: B 67 ARG cc_start: 0.7156 (mmp80) cc_final: 0.6923 (tpp80) REVERT: B 91 LYS cc_start: 0.9468 (ttmm) cc_final: 0.9164 (ttmt) REVERT: D 51 ASP cc_start: 0.9007 (p0) cc_final: 0.8466 (p0) REVERT: D 83 TYR cc_start: 0.7588 (m-10) cc_final: 0.7374 (m-80) REVERT: E 57 SER cc_start: 0.9318 (p) cc_final: 0.8742 (p) REVERT: E 59 GLU cc_start: 0.8682 (pm20) cc_final: 0.8050 (pm20) REVERT: F 88 TYR cc_start: 0.8701 (m-10) cc_final: 0.7659 (m-10) REVERT: F 91 LYS cc_start: 0.9330 (tttp) cc_final: 0.9081 (ttmt) REVERT: H 83 TYR cc_start: 0.8429 (m-10) cc_final: 0.8097 (m-10) REVERT: H 85 LYS cc_start: 0.9306 (mttm) cc_final: 0.8914 (mttp) REVERT: C 64 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8580 (tm-30) REVERT: G 41 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8041 (tm-30) outliers start: 23 outliers final: 22 residues processed: 195 average time/residue: 0.1095 time to fit residues: 30.1949 Evaluate side-chains 195 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN M 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.056321 restraints weight = 45265.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.058535 restraints weight = 20532.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.059928 restraints weight = 13194.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.060785 restraints weight = 10349.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.061313 restraints weight = 9086.872| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13661 Z= 0.150 Angle : 0.626 13.329 19704 Z= 0.365 Chirality : 0.040 0.207 2240 Planarity : 0.004 0.037 1478 Dihedral : 30.122 156.994 4171 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.05 % Allowed : 19.56 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.29), residues: 839 helix: 2.73 (0.22), residues: 554 sheet: 1.13 (1.04), residues: 26 loop : -0.70 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 42 TYR 0.019 0.002 TYR B 88 PHE 0.009 0.001 PHE E 78 HIS 0.004 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (13659) covalent geometry : angle 0.62623 / 0.36 (19698) hydrogen bonds : bond 0.04662 / 3.10 ( 768) hydrogen bonds : angle 2.97980 / 2.23 ( 1920) link_TRANS : bond 0.00032 / 0.02 ( 2) link_TRANS : angle 0.37885 / 0.20 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9202 (m-30) cc_final: 0.8902 (m-30) REVERT: A 125 GLN cc_start: 0.8204 (mt0) cc_final: 0.7388 (mt0) REVERT: B 25 ASN cc_start: 0.8567 (m-40) cc_final: 0.7789 (m110) REVERT: B 91 LYS cc_start: 0.9468 (ttmm) cc_final: 0.9156 (ttmt) REVERT: D 51 ASP cc_start: 0.8993 (p0) cc_final: 0.8451 (p0) REVERT: E 57 SER cc_start: 0.9312 (p) cc_final: 0.8735 (p) REVERT: E 59 GLU cc_start: 0.8709 (pm20) cc_final: 0.8085 (pm20) REVERT: F 88 TYR cc_start: 0.8729 (m-10) cc_final: 0.7648 (m-10) REVERT: F 91 LYS cc_start: 0.9335 (tttp) cc_final: 0.9081 (ttmt) REVERT: H 83 TYR cc_start: 0.8438 (m-10) cc_final: 0.8072 (m-10) REVERT: H 85 LYS cc_start: 0.9303 (mttm) cc_final: 0.8915 (mttp) REVERT: C 64 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8588 (tm-30) REVERT: G 41 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8040 (tm-30) outliers start: 21 outliers final: 20 residues processed: 183 average time/residue: 0.1102 time to fit residues: 28.6598 Evaluate side-chains 190 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN M 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.056497 restraints weight = 39977.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.058586 restraints weight = 19223.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.059898 restraints weight = 12754.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.060692 restraints weight = 10163.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.061099 restraints weight = 9017.955| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.339 13661 Z= 0.285 Angle : 0.930 59.199 19704 Z= 0.556 Chirality : 0.040 0.208 2240 Planarity : 0.005 0.139 1478 Dihedral : 30.120 156.986 4171 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.91 % Allowed : 19.69 % Favored : 77.39 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.29), residues: 839 helix: 2.70 (0.22), residues: 554 sheet: 1.13 (1.04), residues: 26 loop : -0.70 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 42 TYR 0.080 0.003 TYR D 83 PHE 0.008 0.001 PHE E 78 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.28 (13659) covalent geometry : angle 0.93052 / 0.56 (19698) hydrogen bonds : bond 0.04682 / 3.11 ( 768) hydrogen bonds : angle 2.97920 / 2.23 ( 1920) link_TRANS : bond 0.00036 / 0.02 ( 2) link_TRANS : angle 0.38164 / 0.21 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.95 seconds wall clock time: 36 minutes 20.94 seconds (2180.94 seconds total)