Starting phenix.real_space_refine on Sun Aug 9 02:57:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zqc_74564/08_2026/9zqc_74564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zqc_74564/08_2026/9zqc_74564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zqc_74564/08_2026/9zqc_74564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zqc_74564/08_2026/9zqc_74564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zqc_74564/08_2026/9zqc_74564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zqc_74564/08_2026/9zqc_74564.map" } resolution = 2.37 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= 0.012 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: 6 Type Number sf(0) Gaussians P 306 5.49 5 S 40 5.16 5 C 9810 2.51 5 N 3125 2.21 5 O 3843 1.98 5 H 14545 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31669 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1730 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "B" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1730 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "C" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1605 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "D" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1605 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1700 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1696 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1372 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "H" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1413 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "I" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3569 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "J" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3583 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 222} Chain breaks: 1 Chain: "K" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1489 Classifications: {'DNA': 47} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 46} Chain: "L" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 3345 Classifications: {'DNA': 106} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 105} Chain: "M" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 4874 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "P" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1958 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 5.16, per 1000 atoms: 0.16 Number of scatterers: 31669 At special positions: 0 Unit cell: (136.62, 135.792, 120.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 306 15.00 O 3843 8.00 N 3125 7.00 C 9810 6.00 H 14545 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS I 47 " - pdb=" SG CYS I 112 " distance=2.04 Simple disulfide: pdb=" SG CYS I 176 " - pdb=" SG CYS I 250 " distance=2.03 Simple disulfide: pdb=" SG CYS J 47 " - pdb=" SG CYS J 112 " distance=2.03 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 250 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 952.8 milliseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 44.4% alpha, 23.2% beta 152 base pairs and 272 stacking pairs defined. Time for finding SS restraints: 6.74 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 45 through 73 removed outlier: 4.224A pdb=" N VAL A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'B' and resid 16 through 22 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 45 through 73 removed outlier: 4.257A pdb=" N VAL B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 90 through 97 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 54 through 83 Processing helix chain 'C' and resid 89 through 101 Processing helix chain 'C' and resid 103 through 123 removed outlier: 3.683A pdb=" N LYS C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 54 through 83 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.753A pdb=" N LYS D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 45 through 58 Processing helix chain 'F' and resid 64 through 80 removed outlier: 4.075A pdb=" N ASP F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE F 79 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 115 Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 32 through 43 Processing helix chain 'G' and resid 51 through 78 removed outlier: 3.694A pdb=" N GLU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 94 Processing helix chain 'H' and resid 26 through 31 removed outlier: 3.513A pdb=" N GLN H 29 " --> pdb=" O ASP H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 51 through 78 removed outlier: 3.691A pdb=" N GLU H 55 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 95 Processing helix chain 'I' and resid 103 through 107 Processing helix chain 'I' and resid 182 through 184 No H-bonds generated for 'chain 'I' and resid 182 through 184' Processing helix chain 'I' and resid 216 through 219 Processing helix chain 'I' and resid 241 through 245 Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 182 through 184 No H-bonds generated for 'chain 'J' and resid 182 through 184' Processing helix chain 'J' and resid 241 through 245 Processing helix chain 'P' and resid 168 through 185 removed outlier: 3.518A pdb=" N ALA P 172 " --> pdb=" O ASN P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 7.226A pdb=" N ARG A 42 " --> pdb=" O ILE C 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.911A pdb=" N THR A 101 " --> pdb=" O TYR G 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 7.152A pdb=" N ARG B 42 " --> pdb=" O ILE D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.976A pdb=" N THR B 101 " --> pdb=" O TYR H 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.876A pdb=" N ARG E 84 " --> pdb=" O VAL G 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.885A pdb=" N ARG F 84 " --> pdb=" O VAL H 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 119 through 120 Processing sheet with id=AB2, first strand: chain 'I' and resid 28 through 31 Processing sheet with id=AB3, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.776A pdb=" N MET I 35 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYS I 131 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA I 37 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE I 72 " --> pdb=" O TRP I 59 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN I 61 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N THR I 70 " --> pdb=" O GLN I 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.776A pdb=" N MET I 35 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYS I 131 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA I 37 " --> pdb=" O LYS I 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 157 through 160 Processing sheet with id=AB6, first strand: chain 'I' and resid 164 through 166 removed outlier: 6.471A pdb=" N ILE I 188 " --> pdb=" O TYR I 204 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR I 204 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP I 190 " --> pdb=" O ILE I 202 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 164 through 166 removed outlier: 3.831A pdb=" N TYR I 263 " --> pdb=" O ARG I 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 28 through 31 removed outlier: 5.914A pdb=" N GLN J 93 " --> pdb=" O ALA J 49 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLN J 51 " --> pdb=" O SER J 91 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N SER J 91 " --> pdb=" O GLN J 51 " (cutoff:3.500A) removed outlier: 11.832A pdb=" N ILE J 53 " --> pdb=" O SER J 89 " (cutoff:3.500A) removed outlier: 11.662A pdb=" N SER J 89 " --> pdb=" O ILE J 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.747A pdb=" N MET J 35 " --> pdb=" O GLU J 129 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LYS J 131 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA J 37 " --> pdb=" O LYS J 131 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TRP J 59 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.747A pdb=" N MET J 35 " --> pdb=" O GLU J 129 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LYS J 131 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA J 37 " --> pdb=" O LYS J 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 157 through 160 Processing sheet with id=AC3, first strand: chain 'J' and resid 164 through 166 removed outlier: 6.546A pdb=" N ILE J 188 " --> pdb=" O TYR J 204 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR J 204 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP J 190 " --> pdb=" O ILE J 202 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 164 through 166 removed outlier: 3.897A pdb=" N TYR J 263 " --> pdb=" O ARG J 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 106 through 107 Processing sheet with id=AC6, first strand: chain 'P' and resid 106 through 107 611 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 390 hydrogen bonds 780 hydrogen bond angles 0 basepair planarities 152 basepair parallelities 272 stacking parallelities Total time for adding SS restraints: 9.21 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14542 1.03 - 1.23: 222 1.23 - 1.43: 8144 1.43 - 1.62: 9640 1.62 - 1.82: 69 Bond restraints: 32617 Sorted by residual: bond pdb=" C1' DC L 66 " pdb=" N1 DC L 66 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.01e+00 bond pdb=" C3' DT M 10 " pdb=" C2' DT M 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.22e+00 bond pdb=" C3' DC L 51 " pdb=" C2' DC L 51 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.04e+00 bond pdb=" C3' DC L 9 " pdb=" C2' DC L 9 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.61e+00 bond pdb=" C3' DG M 55 " pdb=" C2' DG M 55 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.55e+00 ... (remaining 32612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 57946 2.12 - 4.23: 1054 4.23 - 6.35: 17 6.35 - 8.46: 2 8.46 - 10.58: 6 Bond angle restraints: 59025 Sorted by residual: angle pdb=" N3 DT L 103 " pdb=" C4 DT L 103 " pdb=" O4 DT L 103 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT M 82 " pdb=" C4 DT M 82 " pdb=" O4 DT M 82 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT K 5 " pdb=" C4 DT K 5 " pdb=" O4 DT K 5 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT K 18 " pdb=" C4 DT K 18 " pdb=" O4 DT K 18 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT L 101 " pdb=" C4 DT L 101 " pdb=" O4 DT L 101 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 59020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.93: 12097 32.93 - 65.85: 1954 65.85 - 98.78: 42 98.78 - 131.71: 0 131.71 - 164.64: 3 Dihedral angle restraints: 14096 sinusoidal: 9523 harmonic: 4573 Sorted by residual: dihedral pdb=" CA SER I 118 " pdb=" C SER I 118 " pdb=" N PRO I 119 " pdb=" CA PRO I 119 " ideal model delta harmonic sigma weight residual -180.00 -147.20 -32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" C4' DG L 84 " pdb=" C3' DG L 84 " pdb=" O3' DG L 84 " pdb=" P DT L 85 " ideal model delta sinusoidal sigma weight residual 220.00 55.36 164.64 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG M 97 " pdb=" C3' DG M 97 " pdb=" O3' DG M 97 " pdb=" P DG M 98 " ideal model delta sinusoidal sigma weight residual 220.00 63.26 156.74 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 14093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2454 0.084 - 0.167: 400 0.167 - 0.251: 16 0.251 - 0.334: 0 0.334 - 0.418: 2 Chirality restraints: 2872 Sorted by residual: chirality pdb=" P DC K 4 " pdb=" OP1 DC K 4 " pdb=" OP2 DC K 4 " pdb=" O5' DC K 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.75 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" P DA M 4 " pdb=" OP1 DA M 4 " pdb=" OP2 DA M 4 " pdb=" O5' DA M 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.74 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C3' DA L 69 " pdb=" C4' DA L 69 " pdb=" O3' DA L 69 " pdb=" C2' DA L 69 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.08e-01 ... (remaining 2869 not shown) Planarity restraints: 3738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 118 " -0.089 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO I 119 " 0.231 5.00e-02 4.00e+02 pdb=" CA PRO I 119 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO I 119 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 30 " -0.222 9.50e-02 1.11e+02 7.42e-02 6.69e+00 pdb=" NE ARG D 30 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG D 30 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 30 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 30 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 30 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG D 30 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 30 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 30 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 42 " 0.178 9.50e-02 1.11e+02 5.95e-02 4.23e+00 pdb=" NE ARG J 42 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG J 42 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG J 42 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG J 42 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG J 42 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG J 42 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG J 42 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG J 42 " 0.000 2.00e-02 2.50e+03 ... (remaining 3735 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 9996 2.36 - 2.92: 65473 2.92 - 3.48: 80289 3.48 - 4.04: 120901 4.04 - 4.60: 168799 Nonbonded interactions: 445458 Sorted by model distance: nonbonded pdb=" HG2 ARG J 42 " pdb="HH11 ARG J 42 " model vdw 1.803 2.270 nonbonded pdb=" HG SER A 18 " pdb=" H VAL A 27 " model vdw 1.804 2.100 nonbonded pdb=" HZ2 TRP J 201 " pdb=" HD2 TYR J 204 " model vdw 1.807 2.100 nonbonded pdb=" HZ2 TRP I 201 " pdb=" HD2 TYR I 204 " model vdw 1.820 2.100 nonbonded pdb="HH22 ARG A 20 " pdb=" HE3 LYS C 124 " model vdw 1.836 2.270 ... (remaining 445453 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 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 37 through 135) selection = (chain 'F' and (resid 37 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 115 through 135)) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 22 through 104) } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 23 through 274) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.480 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: 0.150 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 37.930 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.006 0.043 18076 Z= 0.462 Angle : 0.727 10.579 25713 Z= 0.578 Chirality : 0.059 0.418 2872 Planarity : 0.006 0.134 2191 Dihedral : 25.453 164.635 7542 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.01 % Favored : 97.91 % Rotamer: Outliers : 0.86 % Allowed : 14.85 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.24), residues: 1342 helix: 2.45 (0.22), residues: 558 sheet: 0.13 (0.34), residues: 244 loop : 0.37 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 30 TYR 0.015 0.001 TYR I 73 PHE 0.010 0.001 PHE P 126 TRP 0.006 0.001 TRP J 190 HIS 0.002 0.001 HIS P 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.46 (18072) covalent geometry : angle 0.72691 / 0.58 (25705) SS BOND : bond 0.00270 / 0.14 ( 4) SS BOND : angle 0.45702 / 0.21 ( 8) hydrogen bonds : bond 0.11709 / 8.07 ( 977) hydrogen bonds : angle 5.40112 / 3.79 ( 2439) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.9026 (tt0) cc_final: 0.8661 (tt0) REVERT: A 73 ASN cc_start: 0.8823 (t0) cc_final: 0.8135 (t0) REVERT: E 60 GLU cc_start: 0.8798 (pm20) cc_final: 0.8461 (pm20) REVERT: F 60 GLU cc_start: 0.8947 (pm20) cc_final: 0.8649 (pm20) REVERT: H 97 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8118 (mtp-110) REVERT: I 74 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8385 (t80) outliers start: 10 outliers final: 6 residues processed: 181 average time/residue: 1.4666 time to fit residues: 290.3699 Evaluate side-chains 173 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 227 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 126 GLN P 159 GLN P 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.091502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.065385 restraints weight = 85421.402| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.72 r_work: 0.3001 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18076 Z= 0.286 Angle : 0.657 7.671 25713 Z= 0.391 Chirality : 0.044 0.284 2872 Planarity : 0.006 0.136 2191 Dihedral : 28.525 168.242 4871 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 1.46 % Allowed : 15.36 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.23), residues: 1342 helix: 2.37 (0.22), residues: 564 sheet: 0.53 (0.34), residues: 253 loop : 0.08 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 30 TYR 0.021 0.002 TYR I 73 PHE 0.010 0.001 PHE F 68 TRP 0.006 0.001 TRP P 148 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.29 (18072) covalent geometry : angle 0.65705 / 0.39 (25705) SS BOND : bond 0.00774 / 0.40 ( 4) SS BOND : angle 0.90910 / 0.38 ( 8) hydrogen bonds : bond 0.05748 / 3.88 ( 977) hydrogen bonds : angle 4.18252 / 2.93 ( 2439) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.9052 (tt0) cc_final: 0.8749 (tt0) REVERT: A 73 ASN cc_start: 0.8733 (t0) cc_final: 0.8046 (t0) REVERT: B 41 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: B 90 ASP cc_start: 0.9044 (t0) cc_final: 0.8821 (t0) REVERT: E 60 GLU cc_start: 0.8605 (pm20) cc_final: 0.8245 (pm20) REVERT: F 60 GLU cc_start: 0.8696 (pm20) cc_final: 0.8326 (pm20) REVERT: H 97 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8260 (mtp-110) outliers start: 17 outliers final: 8 residues processed: 175 average time/residue: 1.4406 time to fit residues: 276.3505 Evaluate side-chains 170 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain P residue 204 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 128 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN C 94 GLN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066742 restraints weight = 85093.435| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.68 r_work: 0.3016 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18076 Z= 0.176 Angle : 0.606 7.692 25713 Z= 0.368 Chirality : 0.041 0.283 2872 Planarity : 0.005 0.134 2191 Dihedral : 28.638 169.094 4865 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 1.29 % Allowed : 15.45 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.23), residues: 1342 helix: 2.46 (0.22), residues: 564 sheet: 0.67 (0.34), residues: 253 loop : 0.06 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.017 0.001 TYR I 73 PHE 0.017 0.001 PHE P 180 TRP 0.005 0.001 TRP I 190 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.18 (18072) covalent geometry : angle 0.60614 / 0.37 (25705) SS BOND : bond 0.00521 / 0.27 ( 4) SS BOND : angle 0.83874 / 0.35 ( 8) hydrogen bonds : bond 0.04462 / 3.02 ( 977) hydrogen bonds : angle 3.96022 / 2.78 ( 2439) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.9056 (tt0) cc_final: 0.8742 (tt0) REVERT: A 73 ASN cc_start: 0.8695 (t0) cc_final: 0.8024 (t0) REVERT: B 90 ASP cc_start: 0.9024 (t0) cc_final: 0.8722 (t0) REVERT: E 60 GLU cc_start: 0.8604 (pm20) cc_final: 0.8244 (pm20) REVERT: E 121 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8187 (mtt) REVERT: F 60 GLU cc_start: 0.8668 (pm20) cc_final: 0.8284 (pm20) REVERT: I 159 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7921 (mm-40) outliers start: 15 outliers final: 5 residues processed: 177 average time/residue: 1.4619 time to fit residues: 283.6267 Evaluate side-chains 169 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 93 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 125 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.093140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.067240 restraints weight = 84750.187| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.71 r_work: 0.3036 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18076 Z= 0.161 Angle : 0.595 6.873 25713 Z= 0.360 Chirality : 0.040 0.283 2872 Planarity : 0.005 0.133 2191 Dihedral : 28.681 169.469 4860 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 1.03 % Allowed : 15.54 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.23), residues: 1342 helix: 2.58 (0.22), residues: 564 sheet: 0.74 (0.34), residues: 253 loop : 0.11 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 30 TYR 0.016 0.001 TYR I 73 PHE 0.011 0.001 PHE P 180 TRP 0.006 0.001 TRP P 188 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (18072) covalent geometry : angle 0.59510 / 0.36 (25705) SS BOND : bond 0.00521 / 0.27 ( 4) SS BOND : angle 0.66857 / 0.29 ( 8) hydrogen bonds : bond 0.04074 / 2.75 ( 977) hydrogen bonds : angle 3.78302 / 2.65 ( 2439) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8957 (tp30) cc_final: 0.8498 (tp30) REVERT: B 41 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: B 90 ASP cc_start: 0.9008 (t0) cc_final: 0.8704 (t0) REVERT: E 60 GLU cc_start: 0.8598 (pm20) cc_final: 0.8268 (pm20) REVERT: F 60 GLU cc_start: 0.8662 (pm20) cc_final: 0.8462 (pm20) REVERT: H 97 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8114 (mtp-110) REVERT: I 159 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7948 (mm-40) outliers start: 12 outliers final: 6 residues processed: 176 average time/residue: 1.4380 time to fit residues: 277.4915 Evaluate side-chains 170 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain P residue 117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.092770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.067001 restraints weight = 85350.749| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.69 r_work: 0.3019 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18076 Z= 0.179 Angle : 0.600 7.781 25713 Z= 0.360 Chirality : 0.040 0.281 2872 Planarity : 0.005 0.132 2191 Dihedral : 28.712 169.824 4860 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 1.46 % Allowed : 15.97 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.23), residues: 1342 helix: 2.63 (0.22), residues: 564 sheet: 0.71 (0.34), residues: 254 loop : 0.08 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 42 TYR 0.017 0.001 TYR I 73 PHE 0.010 0.001 PHE P 180 TRP 0.005 0.001 TRP I 190 HIS 0.003 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (18072) covalent geometry : angle 0.59959 / 0.36 (25705) SS BOND : bond 0.00541 / 0.28 ( 4) SS BOND : angle 0.66373 / 0.30 ( 8) hydrogen bonds : bond 0.04238 / 2.85 ( 977) hydrogen bonds : angle 3.67873 / 2.58 ( 2439) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.9066 (tt0) cc_final: 0.8769 (tt0) REVERT: A 91 GLU cc_start: 0.8984 (tp30) cc_final: 0.8492 (tp30) REVERT: B 41 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: E 60 GLU cc_start: 0.8609 (pm20) cc_final: 0.8322 (pm20) REVERT: H 97 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8104 (mtp-110) REVERT: I 159 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7954 (mm-40) outliers start: 17 outliers final: 9 residues processed: 182 average time/residue: 1.4998 time to fit residues: 298.7984 Evaluate side-chains 176 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 119 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.091886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.065990 restraints weight = 85039.020| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.69 r_work: 0.2710 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18076 Z= 0.234 Angle : 0.622 8.156 25713 Z= 0.368 Chirality : 0.042 0.281 2872 Planarity : 0.005 0.133 2191 Dihedral : 28.767 170.656 4860 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 1.72 % Allowed : 15.97 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.23), residues: 1342 helix: 2.59 (0.22), residues: 564 sheet: 0.70 (0.34), residues: 254 loop : 0.02 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.020 0.001 TYR I 73 PHE 0.010 0.001 PHE F 68 TRP 0.005 0.001 TRP P 148 HIS 0.004 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (18072) covalent geometry : angle 0.62211 / 0.37 (25705) SS BOND : bond 0.00623 / 0.32 ( 4) SS BOND : angle 0.82410 / 0.35 ( 8) hydrogen bonds : bond 0.04767 / 3.19 ( 977) hydrogen bonds : angle 3.64167 / 2.56 ( 2439) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.9033 (tp30) cc_final: 0.8528 (tp30) REVERT: B 41 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: B 73 ASN cc_start: 0.8796 (t0) cc_final: 0.8562 (t0) REVERT: E 60 GLU cc_start: 0.8611 (pm20) cc_final: 0.8280 (pm20) REVERT: F 60 GLU cc_start: 0.8720 (pm20) cc_final: 0.8427 (pm20) REVERT: I 159 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7979 (mm-40) outliers start: 20 outliers final: 11 residues processed: 181 average time/residue: 1.4740 time to fit residues: 293.5499 Evaluate side-chains 177 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 47 CYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 145 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 68 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.091519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.065655 restraints weight = 85117.795| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.69 r_work: 0.2699 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18076 Z= 0.245 Angle : 0.628 8.736 25713 Z= 0.370 Chirality : 0.042 0.282 2872 Planarity : 0.005 0.133 2191 Dihedral : 28.856 171.867 4860 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 1.37 % Allowed : 16.31 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.23), residues: 1342 helix: 2.52 (0.22), residues: 564 sheet: 0.74 (0.34), residues: 254 loop : -0.01 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 42 TYR 0.021 0.001 TYR I 73 PHE 0.010 0.001 PHE F 68 TRP 0.006 0.001 TRP J 190 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.25 (18072) covalent geometry : angle 0.62832 / 0.37 (25705) SS BOND : bond 0.00616 / 0.32 ( 4) SS BOND : angle 0.80537 / 0.34 ( 8) hydrogen bonds : bond 0.04853 / 3.24 ( 977) hydrogen bonds : angle 3.60402 / 2.55 ( 2439) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.9054 (tp30) cc_final: 0.8541 (tp30) REVERT: E 60 GLU cc_start: 0.8656 (pm20) cc_final: 0.8320 (pm20) REVERT: F 57 LYS cc_start: 0.9290 (ttmm) cc_final: 0.9038 (ttpp) REVERT: F 60 GLU cc_start: 0.8744 (pm20) cc_final: 0.8405 (pm20) REVERT: I 159 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7966 (mm-40) outliers start: 16 outliers final: 9 residues processed: 178 average time/residue: 1.3974 time to fit residues: 273.1436 Evaluate side-chains 173 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 145 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 18 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.092313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.066490 restraints weight = 85205.238| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.69 r_work: 0.2723 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18076 Z= 0.170 Angle : 0.607 9.495 25713 Z= 0.361 Chirality : 0.040 0.282 2872 Planarity : 0.005 0.131 2191 Dihedral : 28.871 171.934 4859 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 1.46 % Allowed : 16.05 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.23), residues: 1342 helix: 2.59 (0.22), residues: 564 sheet: 0.72 (0.34), residues: 254 loop : 0.07 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 30 TYR 0.017 0.001 TYR I 73 PHE 0.010 0.001 PHE F 68 TRP 0.005 0.001 TRP I 190 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (18072) covalent geometry : angle 0.60676 / 0.36 (25705) SS BOND : bond 0.00249 / 0.13 ( 4) SS BOND : angle 1.20132 / 0.62 ( 8) hydrogen bonds : bond 0.04133 / 2.78 ( 977) hydrogen bonds : angle 3.54961 / 2.51 ( 2439) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.9025 (tp30) cc_final: 0.8539 (tp30) REVERT: B 73 ASN cc_start: 0.8778 (t0) cc_final: 0.8525 (t0) REVERT: E 60 GLU cc_start: 0.8638 (pm20) cc_final: 0.8312 (pm20) REVERT: E 74 GLU cc_start: 0.8873 (tt0) cc_final: 0.8497 (tt0) REVERT: F 60 GLU cc_start: 0.8755 (pm20) cc_final: 0.8416 (pm20) REVERT: H 97 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8265 (mtp-110) REVERT: I 159 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7965 (mm-40) REVERT: P 135 GLN cc_start: 0.8304 (mt0) cc_final: 0.8058 (mt0) REVERT: P 136 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6571 (tp) outliers start: 17 outliers final: 9 residues processed: 180 average time/residue: 1.3863 time to fit residues: 273.1056 Evaluate side-chains 177 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 145 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 149 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.092734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.066645 restraints weight = 84901.372| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.71 r_work: 0.2729 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18076 Z= 0.165 Angle : 0.599 9.351 25713 Z= 0.356 Chirality : 0.040 0.282 2872 Planarity : 0.005 0.130 2191 Dihedral : 28.879 171.908 4859 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 1.29 % Allowed : 16.48 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.23), residues: 1342 helix: 2.62 (0.22), residues: 564 sheet: 0.73 (0.34), residues: 254 loop : 0.12 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 30 TYR 0.016 0.001 TYR I 73 PHE 0.009 0.001 PHE P 180 TRP 0.005 0.001 TRP P 148 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (18072) covalent geometry : angle 0.59892 / 0.36 (25705) SS BOND : bond 0.00371 / 0.19 ( 4) SS BOND : angle 1.05108 / 0.56 ( 8) hydrogen bonds : bond 0.03876 / 2.61 ( 977) hydrogen bonds : angle 3.49462 / 2.47 ( 2439) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.9055 (tp30) cc_final: 0.8541 (tp30) REVERT: B 73 ASN cc_start: 0.8764 (t0) cc_final: 0.8541 (t0) REVERT: E 60 GLU cc_start: 0.8624 (pm20) cc_final: 0.8333 (pm20) REVERT: E 74 GLU cc_start: 0.8891 (tt0) cc_final: 0.8554 (tt0) REVERT: F 60 GLU cc_start: 0.8763 (pm20) cc_final: 0.8417 (pm20) REVERT: H 97 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8258 (mtp-110) REVERT: I 159 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7964 (mm-40) outliers start: 15 outliers final: 9 residues processed: 184 average time/residue: 1.4184 time to fit residues: 286.2929 Evaluate side-chains 177 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 145 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 48 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.093070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.067232 restraints weight = 85198.225| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.70 r_work: 0.2740 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18076 Z= 0.140 Angle : 0.597 9.836 25713 Z= 0.355 Chirality : 0.040 0.281 2872 Planarity : 0.006 0.129 2191 Dihedral : 28.870 171.651 4859 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 1.03 % Allowed : 16.48 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: 2.00 (0.23), residues: 1342 helix: 2.67 (0.22), residues: 564 sheet: 0.82 (0.35), residues: 245 loop : 0.15 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 30 TYR 0.014 0.001 TYR I 73 PHE 0.009 0.001 PHE F 68 TRP 0.007 0.001 TRP I 190 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (18072) covalent geometry : angle 0.59736 / 0.35 (25705) SS BOND : bond 0.00374 / 0.19 ( 4) SS BOND : angle 0.79344 / 0.42 ( 8) hydrogen bonds : bond 0.03690 / 2.49 ( 977) hydrogen bonds : angle 3.45499 / 2.44 ( 2439) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.9022 (tp30) cc_final: 0.8561 (tp30) REVERT: B 73 ASN cc_start: 0.8765 (t0) cc_final: 0.8512 (t0) REVERT: B 90 ASP cc_start: 0.8945 (t0) cc_final: 0.8658 (t0) REVERT: E 60 GLU cc_start: 0.8614 (pm20) cc_final: 0.8324 (pm20) REVERT: E 74 GLU cc_start: 0.8890 (tt0) cc_final: 0.8546 (tt0) REVERT: F 60 GLU cc_start: 0.8765 (pm20) cc_final: 0.8426 (pm20) REVERT: H 97 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8258 (mtp-110) REVERT: I 118 SER cc_start: 0.8583 (t) cc_final: 0.8374 (p) REVERT: I 159 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7972 (mm-40) outliers start: 12 outliers final: 9 residues processed: 182 average time/residue: 1.3351 time to fit residues: 266.5410 Evaluate side-chains 181 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 145 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 144 ASN P 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.089831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.063930 restraints weight = 82686.819| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.70 r_work: 0.2826 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18076 Z= 0.160 Angle : 0.596 9.303 25713 Z= 0.354 Chirality : 0.040 0.279 2872 Planarity : 0.005 0.128 2191 Dihedral : 28.846 171.087 4859 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 0.77 % Allowed : 16.91 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: 2.04 (0.23), residues: 1342 helix: 2.68 (0.22), residues: 564 sheet: 0.80 (0.34), residues: 261 loop : 0.21 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 30 TYR 0.016 0.001 TYR I 73 PHE 0.009 0.001 PHE F 68 TRP 0.004 0.001 TRP I 190 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (18072) covalent geometry : angle 0.59548 / 0.35 (25705) SS BOND : bond 0.00369 / 0.19 ( 4) SS BOND : angle 0.88019 / 0.46 ( 8) hydrogen bonds : bond 0.03912 / 2.63 ( 977) hydrogen bonds : angle 3.40252 / 2.41 ( 2439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13525.95 seconds wall clock time: 228 minutes 46.14 seconds (13726.14 seconds total)