Starting phenix.real_space_refine on Mon Jul 6 02:42:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zqc_74564/07_2026/9zqc_74564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zqc_74564/07_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_74564/07_2026/9zqc_74564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zqc_74564/07_2026/9zqc_74564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zqc_74564/07_2026/9zqc_74564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zqc_74564/07_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-dev-6108/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: 4.96, 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: 3.09 Conformation dependent library (CDL) restraints added in 685.8 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: 6.16 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: 8.04 Time building geometry restraints manager: 4.29 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: 57947 2.12 - 4.23: 1053 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.610 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.650 ------------------------------------------------------------------------------- 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= 0.461 Angle : 0.722 10.579 25713 Z= 0.573 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 0.72174 / 0.57 (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 : 0.732 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: 1.5166 time to fit residues: 299.4998 Evaluate side-chains 172 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.091455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.065390 restraints weight = 85432.971| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.76 r_work: 0.3001 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18076 Z= 0.291 Angle : 0.656 7.678 25713 Z= 0.391 Chirality : 0.044 0.276 2872 Planarity : 0.006 0.136 2191 Dihedral : 28.563 169.053 4871 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 1.46 % Allowed : 15.45 % Favored : 83.09 % 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: 1.67 (0.23), residues: 1342 helix: 2.36 (0.22), residues: 564 sheet: 0.55 (0.34), residues: 253 loop : 0.07 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 30 TYR 0.021 0.002 TYR I 73 PHE 0.011 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 0.00599 / 0.29 (18072) covalent geometry : angle 0.65542 / 0.39 (25705) SS BOND : bond 0.00788 / 0.41 ( 4) SS BOND : angle 0.92564 / 0.39 ( 8) hydrogen bonds : bond 0.05696 / 3.84 ( 977) hydrogen bonds : angle 4.15363 / 2.91 ( 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 179 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.764 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: 0.9051 (tt0) cc_final: 0.8750 (tt0) REVERT: A 73 ASN cc_start: 0.8732 (t0) cc_final: 0.8072 (t0) REVERT: B 41 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: B 90 ASP cc_start: 0.9048 (t0) cc_final: 0.8819 (t0) REVERT: E 60 GLU cc_start: 0.8604 (pm20) cc_final: 0.8243 (pm20) REVERT: F 60 GLU cc_start: 0.8691 (pm20) cc_final: 0.8322 (pm20) REVERT: H 97 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8342 (mtp-110) outliers start: 17 outliers final: 7 residues processed: 174 average time/residue: 1.5523 time to fit residues: 295.7671 Evaluate side-chains 167 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLU 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: 5.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.092791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.066769 restraints weight = 85071.586| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.73 r_work: 0.3029 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.0612 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= 0.167 Angle : 0.599 8.537 25713 Z= 0.366 Chirality : 0.041 0.261 2872 Planarity : 0.005 0.134 2191 Dihedral : 28.657 169.927 4864 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.31 % Favored : 97.62 % Rotamer: Outliers : 1.46 % Allowed : 15.11 % 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: 1.78 (0.23), residues: 1342 helix: 2.47 (0.22), residues: 564 sheet: 0.66 (0.34), residues: 253 loop : 0.07 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.016 0.001 TYR I 73 PHE 0.016 0.001 PHE P 180 TRP 0.006 0.001 TRP I 190 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 (18072) covalent geometry : angle 0.59871 / 0.37 (25705) SS BOND : bond 0.00553 / 0.29 ( 4) SS BOND : angle 0.79651 / 0.33 ( 8) hydrogen bonds : bond 0.04417 / 2.98 ( 977) hydrogen bonds : angle 3.96961 / 2.79 ( 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 184 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.588 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: 0.9061 (tt0) cc_final: 0.8753 (tt0) REVERT: B 90 ASP cc_start: 0.9033 (t0) cc_final: 0.8737 (t0) REVERT: E 60 GLU cc_start: 0.8603 (pm20) cc_final: 0.8246 (pm20) REVERT: E 121 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8231 (mtt) REVERT: F 60 GLU cc_start: 0.8670 (pm20) cc_final: 0.8291 (pm20) REVERT: H 97 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8277 (mtp-110) REVERT: I 159 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7930 (mm-40) outliers start: 17 outliers final: 6 residues processed: 178 average time/residue: 1.5281 time to fit residues: 297.4829 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 : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR 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 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 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: 6.9990 chunk 98 optimal weight: 3.9990 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: 1.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN ** 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 = 0.3612 r_free = 0.3612 target = 0.092321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.066519 restraints weight = 84931.290| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.68 r_work: 0.3012 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18076 Z= 0.205 Angle : 0.605 7.129 25713 Z= 0.366 Chirality : 0.041 0.263 2872 Planarity : 0.005 0.134 2191 Dihedral : 28.735 171.045 4864 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.24 % Rotamer: Outliers : 1.03 % Allowed : 15.97 % Favored : 83.00 % 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: 1.82 (0.23), residues: 1342 helix: 2.53 (0.22), residues: 564 sheet: 0.71 (0.34), residues: 253 loop : 0.03 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 30 TYR 0.018 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 0.00407 / 0.21 (18072) covalent geometry : angle 0.60496 / 0.37 (25705) SS BOND : bond 0.00590 / 0.31 ( 4) SS BOND : angle 0.82146 / 0.35 ( 8) hydrogen bonds : bond 0.04549 / 3.06 ( 977) hydrogen bonds : angle 3.81556 / 2.68 ( 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 178 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: E 60 GLU cc_start: 0.8598 (pm20) cc_final: 0.8266 (pm20) REVERT: F 60 GLU cc_start: 0.8672 (pm20) cc_final: 0.8298 (pm20) REVERT: I 159 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7922 (mm-40) REVERT: P 159 GLN cc_start: 0.7717 (mp-120) cc_final: 0.7229 (mt0) outliers start: 12 outliers final: 8 residues processed: 174 average time/residue: 1.5754 time to fit residues: 300.7003 Evaluate side-chains 170 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 D residue 104 GLU 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: 0.9980 chunk 27 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.092858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.067005 restraints weight = 85040.436| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.71 r_work: 0.3020 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0822 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= 0.171 Angle : 0.591 7.477 25713 Z= 0.359 Chirality : 0.040 0.262 2872 Planarity : 0.005 0.133 2191 Dihedral : 28.788 171.605 4860 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 1.20 % Allowed : 16.48 % 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: 1.89 (0.23), residues: 1342 helix: 2.60 (0.22), residues: 564 sheet: 0.71 (0.34), residues: 254 loop : 0.07 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 42 TYR 0.016 0.001 TYR I 73 PHE 0.009 0.001 PHE F 68 TRP 0.005 0.001 TRP I 190 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (18072) covalent geometry : angle 0.59084 / 0.36 (25705) SS BOND : bond 0.00512 / 0.27 ( 4) SS BOND : angle 0.62502 / 0.28 ( 8) hydrogen bonds : bond 0.04121 / 2.77 ( 977) hydrogen bonds : angle 3.71482 / 2.61 ( 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 180 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.775 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: E 60 GLU cc_start: 0.8611 (pm20) cc_final: 0.8323 (pm20) REVERT: I 159 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7959 (mm-40) outliers start: 14 outliers final: 8 residues processed: 176 average time/residue: 1.5679 time to fit residues: 302.1958 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 : 0.717 ------------------------------------------------------------------------------- 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 47 CYS 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 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: 5.9990 chunk 153 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 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 = 0.3610 r_free = 0.3610 target = 0.092089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.066211 restraints weight = 85037.253| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.71 r_work: 0.2712 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18076 Z= 0.221 Angle : 0.614 8.426 25713 Z= 0.366 Chirality : 0.041 0.262 2872 Planarity : 0.005 0.133 2191 Dihedral : 28.841 172.495 4860 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.24 % Rotamer: Outliers : 1.46 % Allowed : 16.22 % 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: 1.83 (0.23), residues: 1342 helix: 2.58 (0.22), residues: 564 sheet: 0.70 (0.34), residues: 254 loop : 0.01 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 42 TYR 0.020 0.001 TYR I 73 PHE 0.010 0.001 PHE F 68 TRP 0.005 0.001 TRP J 190 HIS 0.004 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.22 (18072) covalent geometry : angle 0.61428 / 0.37 (25705) SS BOND : bond 0.00611 / 0.32 ( 4) SS BOND : angle 0.78538 / 0.34 ( 8) hydrogen bonds : bond 0.04676 / 3.14 ( 977) hydrogen bonds : angle 3.65422 / 2.57 ( 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 186 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.742 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: 0.9013 (tp30) cc_final: 0.8543 (tp30) REVERT: B 41 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: E 60 GLU cc_start: 0.8600 (pm20) cc_final: 0.8269 (pm20) REVERT: F 60 GLU cc_start: 0.8709 (pm20) cc_final: 0.8424 (pm20) REVERT: I 159 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7975 (mm-40) REVERT: P 126 PHE cc_start: 0.8863 (m-80) cc_final: 0.8562 (m-80) outliers start: 17 outliers final: 10 residues processed: 181 average time/residue: 1.6028 time to fit residues: 317.0618 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 : 0.778 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 139 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 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: 2.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 125 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 = 0.3598 r_free = 0.3598 target = 0.091324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.065463 restraints weight = 85140.176| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.74 r_work: 0.2692 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18076 Z= 0.279 Angle : 0.637 9.322 25713 Z= 0.375 Chirality : 0.042 0.268 2872 Planarity : 0.005 0.135 2191 Dihedral : 28.929 173.985 4860 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 1.46 % Allowed : 16.31 % 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: 1.74 (0.23), residues: 1342 helix: 2.49 (0.22), residues: 564 sheet: 0.74 (0.34), residues: 254 loop : -0.07 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 30 TYR 0.023 0.002 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 P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.28 (18072) covalent geometry : angle 0.63677 / 0.38 (25705) SS BOND : bond 0.00670 / 0.35 ( 4) SS BOND : angle 0.89096 / 0.38 ( 8) hydrogen bonds : bond 0.05227 / 3.49 ( 977) hydrogen bonds : angle 3.64184 / 2.57 ( 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 180 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.771 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: 0.9037 (tp30) cc_final: 0.8524 (tp30) REVERT: B 41 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: E 60 GLU cc_start: 0.8644 (pm20) cc_final: 0.8311 (pm20) REVERT: F 60 GLU cc_start: 0.8738 (pm20) cc_final: 0.8408 (pm20) REVERT: I 159 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7971 (mm-40) outliers start: 17 outliers final: 12 residues processed: 176 average time/residue: 1.5293 time to fit residues: 295.0500 Evaluate side-chains 176 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 136 LEU 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: 0.8980 chunk 148 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 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: 1.3786 ------------------------------------------------------------------------------- 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 = 0.092009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.066130 restraints weight = 85035.133| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.70 r_work: 0.3005 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1027 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= 0.178 Angle : 0.613 10.229 25713 Z= 0.366 Chirality : 0.041 0.260 2872 Planarity : 0.005 0.133 2191 Dihedral : 28.943 174.157 4860 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 1.55 % Allowed : 16.39 % Favored : 82.06 % 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: 1.79 (0.23), residues: 1342 helix: 2.54 (0.22), residues: 564 sheet: 0.72 (0.34), residues: 254 loop : -0.03 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 30 TYR 0.018 0.001 TYR I 73 PHE 0.011 0.001 PHE P 126 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 0.00345 / 0.18 (18072) covalent geometry : angle 0.61319 / 0.37 (25705) SS BOND : bond 0.00483 / 0.25 ( 4) SS BOND : angle 0.58151 / 0.26 ( 8) hydrogen bonds : bond 0.04502 / 3.01 ( 977) hydrogen bonds : angle 3.60483 / 2.55 ( 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: 18 poor density : 166 time to evaluate : 0.739 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: 0.8975 (tp30) cc_final: 0.8479 (tp30) REVERT: E 60 GLU cc_start: 0.8638 (pm20) cc_final: 0.8317 (pm20) REVERT: E 74 GLU cc_start: 0.8885 (tt0) cc_final: 0.8604 (tt0) REVERT: F 60 GLU cc_start: 0.8716 (pm20) cc_final: 0.8380 (pm20) REVERT: I 159 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7961 (mm-40) REVERT: P 165 CYS cc_start: 0.5468 (OUTLIER) cc_final: 0.5234 (p) outliers start: 18 outliers final: 11 residues processed: 180 average time/residue: 1.4594 time to fit residues: 288.2958 Evaluate side-chains 175 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 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 136 LEU Chi-restraints excluded: chain P residue 145 PHE Chi-restraints excluded: chain P residue 165 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 129 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.092559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066501 restraints weight = 84812.451| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.72 r_work: 0.2722 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1042 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= 0.159 Angle : 0.601 8.633 25713 Z= 0.359 Chirality : 0.040 0.261 2872 Planarity : 0.005 0.132 2191 Dihedral : 28.955 174.405 4859 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 1.55 % Allowed : 16.31 % Favored : 82.15 % 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: 0.71 (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 0.015 0.001 TYR I 73 PHE 0.010 0.001 PHE P 126 TRP 0.005 0.001 TRP I 190 HIS 0.004 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (18072) covalent geometry : angle 0.60070 / 0.36 (25705) SS BOND : bond 0.00426 / 0.22 ( 4) SS BOND : angle 1.03901 / 0.53 ( 8) hydrogen bonds : bond 0.03961 / 2.66 ( 977) hydrogen bonds : angle 3.54864 / 2.50 ( 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 185 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.825 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: 0.9027 (tp30) cc_final: 0.8493 (tp30) REVERT: E 60 GLU cc_start: 0.8632 (pm20) cc_final: 0.8342 (pm20) REVERT: E 74 GLU cc_start: 0.8908 (tt0) cc_final: 0.8546 (tt0) REVERT: F 60 GLU cc_start: 0.8723 (pm20) cc_final: 0.8366 (pm20) REVERT: I 159 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7969 (mm-40) REVERT: P 165 CYS cc_start: 0.5441 (OUTLIER) cc_final: 0.5179 (p) outliers start: 18 outliers final: 10 residues processed: 180 average time/residue: 1.4817 time to fit residues: 292.2414 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 : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain P residue 165 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 48 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 135 GLN P 144 ASN ** 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 = 0.3625 r_free = 0.3625 target = 0.093103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.067240 restraints weight = 84890.773| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.72 r_work: 0.2734 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 0.043 18076 Z= 0.148 Angle : 0.599 10.410 25713 Z= 0.357 Chirality : 0.040 0.261 2872 Planarity : 0.007 0.202 2191 Dihedral : 28.951 174.272 4859 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 1.12 % Allowed : 16.74 % Favored : 82.15 % 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: 1.92 (0.23), residues: 1342 helix: 2.63 (0.22), residues: 564 sheet: 0.79 (0.35), residues: 246 loop : 0.06 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 30 TYR 0.014 0.001 TYR I 73 PHE 0.011 0.001 PHE P 126 TRP 0.007 0.001 TRP J 190 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (18072) covalent geometry : angle 0.59815 / 0.36 (25705) SS BOND : bond 0.00309 / 0.16 ( 4) SS BOND : angle 1.54000 / 0.86 ( 8) hydrogen bonds : bond 0.03750 / 2.52 ( 977) hydrogen bonds : angle 3.49973 / 2.47 ( 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 184 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.639 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: 0.9023 (tp30) cc_final: 0.8502 (tp30) REVERT: E 60 GLU cc_start: 0.8612 (pm20) cc_final: 0.8320 (pm20) REVERT: E 74 GLU cc_start: 0.8900 (tt0) cc_final: 0.8528 (tt0) REVERT: F 57 LYS cc_start: 0.9298 (ttmm) cc_final: 0.9062 (ttpp) REVERT: H 97 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8251 (mtp-110) REVERT: I 118 SER cc_start: 0.8664 (t) cc_final: 0.8454 (p) REVERT: I 159 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7972 (mm-40) outliers start: 13 outliers final: 11 residues processed: 181 average time/residue: 1.5538 time to fit residues: 307.4104 Evaluate side-chains 179 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain P residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN P 135 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 = 0.3635 r_free = 0.3635 target = 0.093402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.067438 restraints weight = 84980.747| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.71 r_work: 0.2750 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1146 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= 0.140 Angle : 0.585 9.239 25713 Z= 0.351 Chirality : 0.040 0.262 2872 Planarity : 0.006 0.135 2191 Dihedral : 28.927 173.737 4859 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 1.20 % Allowed : 16.74 % Favored : 82.06 % 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: 2.70 (0.22), residues: 564 sheet: 0.82 (0.35), residues: 246 loop : 0.09 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 30 TYR 0.013 0.001 TYR I 73 PHE 0.010 0.001 PHE P 126 TRP 0.007 0.001 TRP I 190 HIS 0.003 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (18072) covalent geometry : angle 0.58516 / 0.35 (25705) SS BOND : bond 0.00322 / 0.17 ( 4) SS BOND : angle 0.98380 / 0.53 ( 8) hydrogen bonds : bond 0.03589 / 2.42 ( 977) hydrogen bonds : angle 3.42741 / 2.42 ( 2439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13526.72 seconds wall clock time: 228 minutes 58.56 seconds (13738.56 seconds total)