Starting phenix.real_space_refine on Sat Sep 12 21:44:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7af3_11751/09_2026/7af3_11751_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7af3_11751/09_2026/7af3_11751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7af3_11751/09_2026/7af3_11751_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7af3_11751/09_2026/7af3_11751_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7af3_11751/09_2026/7af3_11751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7af3_11751/09_2026/7af3_11751.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 51 5.21 5 S 28 5.16 5 C 9858 2.51 5 N 3453 2.21 5 O 4733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18580 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 37, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 211, 'rna3p_pyr': 171} Link IDs: {'rna2p': 71, 'rna3p': 384} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "I" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 803 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' MG': 51} Classifications: {'undetermined': 51} Link IDs: {None: 50} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.94, per 1000 atoms: 0.16 Number of scatterers: 18580 At special positions: 0 Unit cell: (113.4, 150.15, 126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 51 11.99 O 4733 8.00 N 3453 7.00 C 9858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 590.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 49.9% alpha, 16.5% beta 140 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'C' and resid 8 through 12 Processing helix chain 'C' and resid 25 through 48 removed outlier: 4.574A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.712A pdb=" N VAL C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 95 removed outlier: 3.529A pdb=" N GLU C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 125 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 53 removed outlier: 3.756A pdb=" N ILE G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 67 removed outlier: 3.583A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 3.866A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 129 Processing helix chain 'G' and resid 134 through 148 removed outlier: 3.813A pdb=" N ARG G 138 " --> pdb=" O ALA G 134 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN G 148 " --> pdb=" O MET G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 152 removed outlier: 3.511A pdb=" N ALA G 152 " --> pdb=" O LYS G 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 149 through 152' Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 42 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 94 through 101 Processing helix chain 'J' and resid 14 through 32 removed outlier: 4.260A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 89 removed outlier: 3.552A pdb=" N VAL J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.875A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 61 Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.586A pdb=" N GLU M 72 " --> pdb=" O ASP M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 17 Processing helix chain 'N' and resid 20 through 32 Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.799A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 Proline residue: N 57 - end of helix removed outlier: 3.674A pdb=" N GLN N 60 " --> pdb=" O PRO N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.630A pdb=" N ARG N 90 " --> pdb=" O GLU N 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 26 removed outlier: 3.652A pdb=" N SER S 25 " --> pdb=" O LYS S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 70 through 74 Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 103 through 124 Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.226A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 Processing sheet with id=AA1, first strand: chain 'C' and resid 52 through 58 removed outlier: 6.835A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 164 through 171 removed outlier: 6.471A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AA4, first strand: chain 'I' and resid 6 through 12 removed outlier: 6.084A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 36 through 52 removed outlier: 5.803A pdb=" N GLY J 38 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASP J 75 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU J 42 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 36 through 52 removed outlier: 5.803A pdb=" N GLY J 38 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASP J 75 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU J 42 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 73 through 74 removed outlier: 3.684A pdb=" N LEU N 79 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 31 through 33 Processing sheet with id=AA9, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.568A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.722A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 576 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 4.79 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3060 1.33 - 1.45: 7225 1.45 - 1.57: 8572 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19821 Sorted by residual: bond pdb=" N ILE J 40 " pdb=" CA ILE J 40 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.30e-03 1.88e+04 1.81e+01 bond pdb=" N ILE M 9 " pdb=" CA ILE M 9 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.00e-03 1.23e+04 1.57e+01 bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.461 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" N9 A 11363 " pdb=" C4 A 11363 " ideal model delta sigma weight residual 1.374 1.351 0.023 6.00e-03 2.78e+04 1.48e+01 bond pdb=" C5 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.382 1.457 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 19816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 26792 2.06 - 4.11: 2082 4.11 - 6.17: 82 6.17 - 8.22: 14 8.22 - 10.28: 6 Bond angle restraints: 28976 Sorted by residual: angle pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sigma weight residual 118.80 127.68 -8.88 1.10e+00 8.26e-01 6.52e+01 angle pdb=" N1 C 11158 " pdb=" C2 C 11158 " pdb=" O2 C 11158 " ideal model delta sigma weight residual 118.90 123.37 -4.47 6.00e-01 2.78e+00 5.55e+01 angle pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C6 C 11158 " ideal model delta sigma weight residual 120.80 113.37 7.43 1.20e+00 6.94e-01 3.83e+01 angle pdb=" O5' G 11053 " pdb=" C5' G 11053 " pdb=" C4' G 11053 " ideal model delta sigma weight residual 109.40 114.29 -4.89 8.00e-01 1.56e+00 3.73e+01 angle pdb=" N9 G 11279 " pdb=" C8 G 11279 " pdb=" N7 G 11279 " ideal model delta sigma weight residual 113.10 116.11 -3.01 5.00e-01 4.00e+00 3.62e+01 ... (remaining 28971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.58: 11383 33.58 - 67.15: 1141 67.15 - 100.72: 133 100.72 - 134.30: 4 134.30 - 167.87: 2 Dihedral angle restraints: 12663 sinusoidal: 9484 harmonic: 3179 Sorted by residual: dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual 232.00 64.13 167.87 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" O4' U 11168 " pdb=" C1' U 11168 " pdb=" N1 U 11168 " pdb=" C2 U 11168 " ideal model delta sinusoidal sigma weight residual -128.00 35.77 -163.77 1 1.70e+01 3.46e-03 6.51e+01 dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 200.00 96.91 103.09 1 1.50e+01 4.44e-03 5.23e+01 ... (remaining 12660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2783 0.081 - 0.162: 761 0.162 - 0.243: 61 0.243 - 0.324: 7 0.324 - 0.405: 1 Chirality restraints: 3613 Sorted by residual: chirality pdb=" CA VAL J 57 " pdb=" N VAL J 57 " pdb=" C VAL J 57 " pdb=" CB VAL J 57 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CB VAL J 57 " pdb=" CA VAL J 57 " pdb=" CG1 VAL J 57 " pdb=" CG2 VAL J 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA THR B 125 " pdb=" N THR B 125 " pdb=" C THR B 125 " pdb=" CB THR B 125 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3610 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " 0.008 2.00e-02 2.50e+03 2.57e-02 2.14e+01 pdb=" N9 2MG 11207 " 0.007 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " -0.011 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " -0.016 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " -0.008 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " -0.004 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " -0.014 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " 0.011 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " 0.026 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " 0.038 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " 0.022 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " 0.011 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 1 966 " -0.013 2.00e-02 2.50e+03 2.34e-02 1.78e+01 pdb=" N9 2MG 1 966 " -0.000 2.00e-02 2.50e+03 pdb=" C8 2MG 1 966 " 0.010 2.00e-02 2.50e+03 pdb=" N7 2MG 1 966 " 0.016 2.00e-02 2.50e+03 pdb=" C5 2MG 1 966 " 0.005 2.00e-02 2.50e+03 pdb=" C6 2MG 1 966 " 0.002 2.00e-02 2.50e+03 pdb=" O6 2MG 1 966 " 0.013 2.00e-02 2.50e+03 pdb=" N1 2MG 1 966 " -0.010 2.00e-02 2.50e+03 pdb=" C2 2MG 1 966 " -0.022 2.00e-02 2.50e+03 pdb=" N2 2MG 1 966 " -0.033 2.00e-02 2.50e+03 pdb=" N3 2MG 1 966 " -0.022 2.00e-02 2.50e+03 pdb=" C4 2MG 1 966 " -0.009 2.00e-02 2.50e+03 pdb=" CM2 2MG 1 966 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 112 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.73e+00 pdb=" C GLY G 112 " -0.051 2.00e-02 2.50e+03 pdb=" O GLY G 112 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP G 113 " 0.018 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 105 2.49 - 3.09: 12629 3.09 - 3.69: 33285 3.69 - 4.30: 51405 4.30 - 4.90: 71298 Nonbonded interactions: 168722 Sorted by model distance: nonbonded pdb=" OP2 C 11054 " pdb="MG MG 11616 " model vdw 1.884 2.170 nonbonded pdb=" O6 G 11178 " pdb="MG MG 11611 " model vdw 1.918 2.170 nonbonded pdb=" OP1 G 1 945 " pdb="MG MG 11643 " model vdw 1.936 2.170 nonbonded pdb=" O6 G 11108 " pdb="MG MG 11635 " model vdw 1.936 2.170 nonbonded pdb=" OP1 G 1 993 " pdb="MG MG 11640 " model vdw 1.956 2.170 ... (remaining 168717 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.250 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.300 Find NCS groups from input model: 0.060 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 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 : 0.009 0.151 19822 Z= 0.823 Angle : 1.005 10.277 28976 Z= 0.774 Chirality : 0.069 0.405 3613 Planarity : 0.004 0.030 1998 Dihedral : 21.218 167.874 10605 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.87 % Allowed : 5.42 % Favored : 93.72 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.25), residues: 1095 helix: 0.20 (0.24), residues: 497 sheet: -0.54 (0.39), residues: 166 loop : -0.59 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 53 TYR 0.011 0.002 TYR B 213 PHE 0.010 0.002 PHE S 74 TRP 0.014 0.002 TRP C 201 HIS 0.005 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00912 / 0.82 (19821) covalent geometry : angle 1.00514 / 0.77 (28976) hydrogen bonds : bond 0.18292 / 19.75 ( 785) hydrogen bonds : angle 6.31211 / 8.67 ( 1800) metal coordination : bond 0.15126 / 7.56 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 292 time to evaluate : 0.466 Fit side-chains REVERT: C 211 MET cc_start: 0.6283 (mmm) cc_final: 0.5710 (mmt) REVERT: G 63 GLU cc_start: 0.7731 (mp0) cc_final: 0.7398 (mp0) REVERT: G 76 LYS cc_start: 0.4854 (ttpp) cc_final: 0.4501 (tmmm) REVERT: G 111 ARG cc_start: 0.7467 (tpt170) cc_final: 0.6900 (tpp80) REVERT: G 114 LYS cc_start: 0.6665 (mmtt) cc_final: 0.6136 (pptt) REVERT: G 136 LYS cc_start: 0.7099 (mptt) cc_final: 0.6847 (mptt) REVERT: I 42 GLU cc_start: 0.7644 (tp30) cc_final: 0.7443 (mm-30) REVERT: J 80 THR cc_start: 0.8201 (p) cc_final: 0.7995 (p) REVERT: M 44 LYS cc_start: 0.9089 (mttt) cc_final: 0.8327 (mttt) REVERT: M 50 GLU cc_start: 0.7090 (tp30) cc_final: 0.6795 (tp30) REVERT: N 6 MET cc_start: 0.8975 (mmm) cc_final: 0.8433 (mmm) REVERT: B 96 TRP cc_start: 0.7190 (t-100) cc_final: 0.6940 (t-100) outliers start: 8 outliers final: 4 residues processed: 298 average time/residue: 0.6951 time to fit residues: 230.5312 Evaluate side-chains 187 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 183 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain B residue 167 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 0.0570 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 4 ASN I 32 GLN J 3 ASN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN B 51 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.085404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.060404 restraints weight = 46306.372| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.85 r_work: 0.2801 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19822 Z= 0.136 Angle : 0.568 8.830 28976 Z= 0.327 Chirality : 0.039 0.231 3613 Planarity : 0.005 0.043 1998 Dihedral : 22.191 172.057 8383 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.01 % Allowed : 19.07 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.25), residues: 1095 helix: 0.60 (0.24), residues: 495 sheet: -0.20 (0.40), residues: 160 loop : -0.32 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 81 TYR 0.019 0.002 TYR I 90 PHE 0.015 0.001 PHE I 127 TRP 0.012 0.001 TRP B 96 HIS 0.004 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (19821) covalent geometry : angle 0.56763 / 0.33 (28976) hydrogen bonds : bond 0.06622 / 7.44 ( 785) hydrogen bonds : angle 4.17168 / 5.43 ( 1800) metal coordination : bond 0.01607 / 0.80 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: C 80 LYS cc_start: 0.8763 (mmpt) cc_final: 0.8413 (mmmm) REVERT: C 112 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8062 (t0) REVERT: C 211 MET cc_start: 0.6248 (mmm) cc_final: 0.5610 (mmt) REVERT: G 6 VAL cc_start: 0.5914 (OUTLIER) cc_final: 0.5572 (m) REVERT: G 30 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7748 (pt) REVERT: G 111 ARG cc_start: 0.7414 (tpt170) cc_final: 0.6696 (tpp80) REVERT: G 139 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6473 (pp20) REVERT: I 42 GLU cc_start: 0.8210 (tp30) cc_final: 0.7961 (mm-30) REVERT: J 24 GLU cc_start: 0.8538 (tm-30) cc_final: 0.7954 (tm-30) REVERT: M 44 LYS cc_start: 0.9109 (mttt) cc_final: 0.8474 (mtpt) REVERT: M 50 GLU cc_start: 0.7720 (tp30) cc_final: 0.7268 (tp30) REVERT: M 59 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8635 (tp30) REVERT: B 10 LEU cc_start: 0.4997 (mt) cc_final: 0.4321 (pp) REVERT: B 114 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7318 (pp) REVERT: B 133 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6671 (tt0) REVERT: B 175 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6070 (mt-10) outliers start: 37 outliers final: 11 residues processed: 231 average time/residue: 0.6334 time to fit residues: 164.4815 Evaluate side-chains 206 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 103 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 98 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.1051 > 50:) chunk 94 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 3 GLN I 32 GLN I 110 GLN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN B 103 ASN B 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.083239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.058085 restraints weight = 47073.999| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.84 r_work: 0.2739 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19822 Z= 0.228 Angle : 0.606 8.123 28976 Z= 0.334 Chirality : 0.044 0.254 3613 Planarity : 0.005 0.049 1998 Dihedral : 21.983 173.352 8376 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 6.18 % Allowed : 20.15 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1095 helix: 0.64 (0.23), residues: 506 sheet: 0.13 (0.39), residues: 163 loop : -0.26 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 81 TYR 0.022 0.002 TYR I 90 PHE 0.015 0.002 PHE I 20 TRP 0.013 0.001 TRP C 201 HIS 0.005 0.001 HIS I 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.23 (19821) covalent geometry : angle 0.60561 / 0.33 (28976) hydrogen bonds : bond 0.06168 / 6.83 ( 785) hydrogen bonds : angle 4.01921 / 5.13 ( 1800) metal coordination : bond 0.00144 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 112 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8110 (t0) REVERT: G 21 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: G 30 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7660 (pt) REVERT: G 111 ARG cc_start: 0.7310 (tpt170) cc_final: 0.6423 (tpp80) REVERT: G 139 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6557 (pp20) REVERT: I 42 GLU cc_start: 0.8233 (tp30) cc_final: 0.8004 (mm-30) REVERT: M 44 LYS cc_start: 0.9133 (mttt) cc_final: 0.8669 (mtpm) REVERT: M 50 GLU cc_start: 0.7878 (tp30) cc_final: 0.7469 (tp30) REVERT: M 59 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8750 (tp30) REVERT: B 10 LEU cc_start: 0.4891 (mt) cc_final: 0.4291 (pp) REVERT: B 108 ARG cc_start: 0.8359 (mtp-110) cc_final: 0.8144 (ttp-110) REVERT: B 114 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7261 (pp) REVERT: B 133 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6655 (tt0) REVERT: B 154 MET cc_start: 0.5978 (ttp) cc_final: 0.5452 (mtp) REVERT: B 175 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6613 (mt-10) REVERT: B 227 GLN cc_start: 0.4211 (OUTLIER) cc_final: 0.3736 (pp30) outliers start: 57 outliers final: 26 residues processed: 223 average time/residue: 0.5963 time to fit residues: 149.7221 Evaluate side-chains 213 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 132 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 9 optimal weight: 30.0000 chunk 141 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 32 GLN I 110 GLN B 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.082677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.057693 restraints weight = 46862.314| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.72 r_work: 0.2726 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19822 Z= 0.252 Angle : 0.601 7.848 28976 Z= 0.333 Chirality : 0.044 0.233 3613 Planarity : 0.005 0.051 1998 Dihedral : 21.973 173.118 8376 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 6.07 % Allowed : 20.48 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1095 helix: 0.70 (0.23), residues: 502 sheet: 0.21 (0.39), residues: 166 loop : -0.23 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 95 TYR 0.022 0.002 TYR I 90 PHE 0.014 0.002 PHE I 20 TRP 0.013 0.001 TRP C 201 HIS 0.003 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.25 (19821) covalent geometry : angle 0.60140 / 0.33 (28976) hydrogen bonds : bond 0.05814 / 6.44 ( 785) hydrogen bonds : angle 3.97605 / 5.07 ( 1800) metal coordination : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: C 112 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8095 (t0) REVERT: G 21 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: G 30 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7665 (pt) REVERT: G 36 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7728 (tptp) REVERT: G 111 ARG cc_start: 0.7508 (tpt170) cc_final: 0.6558 (tpp80) REVERT: G 139 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6646 (pp20) REVERT: I 42 GLU cc_start: 0.8259 (tp30) cc_final: 0.8035 (mm-30) REVERT: I 72 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8931 (pp) REVERT: I 91 ASP cc_start: 0.8728 (t0) cc_final: 0.8467 (t0) REVERT: M 44 LYS cc_start: 0.9095 (mttt) cc_final: 0.8527 (mtpm) REVERT: M 50 GLU cc_start: 0.7967 (tp30) cc_final: 0.7555 (tp30) REVERT: N 6 MET cc_start: 0.9320 (mmm) cc_final: 0.8907 (mmm) REVERT: N 92 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7934 (mm-30) REVERT: B 10 LEU cc_start: 0.4813 (mt) cc_final: 0.4180 (pp) REVERT: B 100 MET cc_start: 0.6938 (mtp) cc_final: 0.6589 (mtt) REVERT: B 108 ARG cc_start: 0.8446 (mtp-110) cc_final: 0.8117 (ttp-110) REVERT: B 114 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7381 (pp) REVERT: B 133 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6569 (tt0) REVERT: B 154 MET cc_start: 0.6038 (ttp) cc_final: 0.5711 (mtm) outliers start: 56 outliers final: 26 residues processed: 215 average time/residue: 0.6078 time to fit residues: 146.8038 Evaluate side-chains 209 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 2 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 32 GLN I 110 GLN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 HIS ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.083546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.058490 restraints weight = 46386.912| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.81 r_work: 0.2759 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19822 Z= 0.175 Angle : 0.549 8.994 28976 Z= 0.311 Chirality : 0.039 0.205 3613 Planarity : 0.004 0.041 1998 Dihedral : 21.973 173.071 8376 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer: Outliers : 5.31 % Allowed : 21.13 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.25), residues: 1095 helix: 0.91 (0.23), residues: 500 sheet: 0.24 (0.40), residues: 168 loop : -0.22 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 95 TYR 0.021 0.002 TYR I 6 PHE 0.013 0.001 PHE S 74 TRP 0.013 0.001 TRP C 201 HIS 0.003 0.001 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (19821) covalent geometry : angle 0.54923 / 0.31 (28976) hydrogen bonds : bond 0.05268 / 5.88 ( 785) hydrogen bonds : angle 3.84721 / 4.91 ( 1800) metal coordination : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 112 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8034 (t0) REVERT: G 21 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: G 30 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7721 (pt) REVERT: G 75 VAL cc_start: 0.5629 (OUTLIER) cc_final: 0.5332 (t) REVERT: G 111 ARG cc_start: 0.7473 (tpt170) cc_final: 0.6591 (tpp80) REVERT: G 139 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6810 (pp20) REVERT: I 42 GLU cc_start: 0.8255 (tp30) cc_final: 0.8035 (mm-30) REVERT: I 91 ASP cc_start: 0.8763 (t0) cc_final: 0.8486 (t0) REVERT: J 89 ARG cc_start: 0.8042 (mmp80) cc_final: 0.7819 (mmp80) REVERT: M 44 LYS cc_start: 0.9011 (mttt) cc_final: 0.8374 (mtpt) REVERT: M 50 GLU cc_start: 0.8014 (tp30) cc_final: 0.7585 (tp30) REVERT: N 6 MET cc_start: 0.9294 (mmm) cc_final: 0.8906 (mmm) REVERT: N 92 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: B 10 LEU cc_start: 0.4835 (mt) cc_final: 0.4213 (pp) REVERT: B 100 MET cc_start: 0.7195 (mtp) cc_final: 0.6867 (mtt) REVERT: B 108 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.8147 (ttp-110) REVERT: B 114 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7241 (pp) REVERT: B 133 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6712 (tt0) REVERT: B 154 MET cc_start: 0.6123 (ttp) cc_final: 0.5759 (mtm) outliers start: 49 outliers final: 22 residues processed: 216 average time/residue: 0.6137 time to fit residues: 149.0839 Evaluate side-chains 209 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 32 GLN I 110 GLN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.083966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.059356 restraints weight = 46312.879| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.77 r_work: 0.2781 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19822 Z= 0.151 Angle : 0.532 8.516 28976 Z= 0.301 Chirality : 0.038 0.198 3613 Planarity : 0.004 0.032 1998 Dihedral : 21.955 173.265 8376 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer: Outliers : 4.66 % Allowed : 22.64 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1095 helix: 1.08 (0.23), residues: 500 sheet: 0.60 (0.41), residues: 159 loop : -0.15 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 81 TYR 0.021 0.002 TYR I 6 PHE 0.009 0.001 PHE B 90 TRP 0.013 0.001 TRP C 201 HIS 0.003 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (19821) covalent geometry : angle 0.53248 / 0.30 (28976) hydrogen bonds : bond 0.04994 / 5.58 ( 785) hydrogen bonds : angle 3.78946 / 4.85 ( 1800) metal coordination : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 112 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7950 (t0) REVERT: G 21 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: G 56 LYS cc_start: 0.7678 (tmtt) cc_final: 0.7389 (tmmt) REVERT: G 75 VAL cc_start: 0.5649 (OUTLIER) cc_final: 0.5348 (t) REVERT: G 111 ARG cc_start: 0.7466 (tpt170) cc_final: 0.6624 (tpp80) REVERT: G 139 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6791 (pp20) REVERT: I 42 GLU cc_start: 0.8236 (tp30) cc_final: 0.8028 (mm-30) REVERT: I 91 ASP cc_start: 0.8745 (t0) cc_final: 0.8442 (t0) REVERT: I 119 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8271 (mtp85) REVERT: M 44 LYS cc_start: 0.9038 (mttt) cc_final: 0.8385 (mtpt) REVERT: M 50 GLU cc_start: 0.8090 (tp30) cc_final: 0.7679 (tp30) REVERT: N 6 MET cc_start: 0.9273 (mmm) cc_final: 0.8907 (mmm) REVERT: N 92 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8045 (mm-30) REVERT: B 10 LEU cc_start: 0.4810 (mt) cc_final: 0.4193 (pp) REVERT: B 70 VAL cc_start: 0.6168 (t) cc_final: 0.5838 (t) REVERT: B 100 MET cc_start: 0.7270 (mtp) cc_final: 0.6933 (mtt) REVERT: B 114 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7175 (pp) REVERT: B 133 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: B 142 GLU cc_start: 0.7901 (pp20) cc_final: 0.7565 (pp20) REVERT: B 145 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7873 (pp20) REVERT: B 154 MET cc_start: 0.6115 (ttp) cc_final: 0.5850 (mtt) outliers start: 43 outliers final: 22 residues processed: 214 average time/residue: 0.6036 time to fit residues: 145.4701 Evaluate side-chains 213 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 119 ARG Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 107 optimal weight: 0.1980 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 ASN I 32 GLN I 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.084911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.060156 restraints weight = 46625.848| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.79 r_work: 0.2803 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19822 Z= 0.123 Angle : 0.511 8.935 28976 Z= 0.292 Chirality : 0.036 0.234 3613 Planarity : 0.004 0.031 1998 Dihedral : 21.951 174.100 8376 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.35 % Rotamer: Outliers : 3.79 % Allowed : 24.38 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 1095 helix: 1.18 (0.23), residues: 500 sheet: 0.75 (0.41), residues: 154 loop : -0.11 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 89 TYR 0.020 0.001 TYR I 6 PHE 0.011 0.001 PHE B 90 TRP 0.013 0.001 TRP C 201 HIS 0.002 0.000 HIS C 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (19821) covalent geometry : angle 0.51127 / 0.29 (28976) hydrogen bonds : bond 0.04778 / 5.39 ( 785) hydrogen bonds : angle 3.75584 / 4.84 ( 1800) metal coordination : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7937 (t0) REVERT: G 21 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: G 75 VAL cc_start: 0.5579 (OUTLIER) cc_final: 0.5288 (t) REVERT: G 111 ARG cc_start: 0.7367 (tpt170) cc_final: 0.6585 (tpp80) REVERT: G 137 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7536 (ttpt) REVERT: G 139 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6786 (pp20) REVERT: I 91 ASP cc_start: 0.8732 (t0) cc_final: 0.8417 (t0) REVERT: J 24 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8004 (tm-30) REVERT: M 44 LYS cc_start: 0.9029 (mttt) cc_final: 0.8358 (mtpt) REVERT: M 50 GLU cc_start: 0.8100 (tp30) cc_final: 0.7693 (tp30) REVERT: N 6 MET cc_start: 0.9269 (mmm) cc_final: 0.8924 (mmm) REVERT: N 92 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8050 (mm-30) REVERT: B 10 LEU cc_start: 0.5012 (mt) cc_final: 0.4387 (pp) REVERT: B 70 VAL cc_start: 0.6128 (t) cc_final: 0.5897 (t) REVERT: B 100 MET cc_start: 0.7276 (mtp) cc_final: 0.6922 (mtt) REVERT: B 105 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6615 (pttt) REVERT: B 114 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7185 (pp) REVERT: B 133 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6690 (tt0) REVERT: B 154 MET cc_start: 0.6139 (ttp) cc_final: 0.5744 (mtt) outliers start: 35 outliers final: 16 residues processed: 215 average time/residue: 0.6225 time to fit residues: 149.8519 Evaluate side-chains 213 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 39 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 139 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 ASN I 32 GLN I 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.084680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.059952 restraints weight = 46449.455| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.78 r_work: 0.2796 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19822 Z= 0.139 Angle : 0.522 9.770 28976 Z= 0.294 Chirality : 0.037 0.242 3613 Planarity : 0.004 0.031 1998 Dihedral : 21.904 173.962 8376 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 3.58 % Allowed : 24.81 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1095 helix: 1.20 (0.24), residues: 500 sheet: 0.80 (0.42), residues: 154 loop : -0.06 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 89 TYR 0.009 0.001 TYR B 213 PHE 0.009 0.001 PHE B 90 TRP 0.012 0.001 TRP C 201 HIS 0.002 0.001 HIS C 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (19821) covalent geometry : angle 0.52167 / 0.29 (28976) hydrogen bonds : bond 0.04747 / 5.32 ( 785) hydrogen bonds : angle 3.76116 / 4.85 ( 1800) metal coordination : bond 0.00029 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7963 (t0) REVERT: G 15 ASP cc_start: 0.6563 (t70) cc_final: 0.6306 (t0) REVERT: G 21 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: G 75 VAL cc_start: 0.5669 (OUTLIER) cc_final: 0.5377 (t) REVERT: G 111 ARG cc_start: 0.7450 (tpt170) cc_final: 0.6646 (tpp80) REVERT: G 139 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6787 (pp20) REVERT: I 91 ASP cc_start: 0.8730 (t0) cc_final: 0.8410 (t0) REVERT: M 27 LYS cc_start: 0.8800 (tptm) cc_final: 0.8452 (tppp) REVERT: M 44 LYS cc_start: 0.9074 (mttt) cc_final: 0.8416 (mtpt) REVERT: M 50 GLU cc_start: 0.8179 (tp30) cc_final: 0.7754 (tp30) REVERT: N 6 MET cc_start: 0.9273 (mmm) cc_final: 0.8933 (mmm) REVERT: B 10 LEU cc_start: 0.5088 (mt) cc_final: 0.4497 (pp) REVERT: B 70 VAL cc_start: 0.6183 (t) cc_final: 0.5967 (t) REVERT: B 100 MET cc_start: 0.7317 (mtp) cc_final: 0.6975 (mtt) REVERT: B 133 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6610 (tt0) REVERT: B 142 GLU cc_start: 0.7933 (pp20) cc_final: 0.7664 (pp20) REVERT: B 145 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7875 (pp20) REVERT: B 154 MET cc_start: 0.6194 (ttp) cc_final: 0.5859 (mtt) outliers start: 33 outliers final: 19 residues processed: 216 average time/residue: 0.6008 time to fit residues: 146.5865 Evaluate side-chains 217 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 ASN I 32 GLN I 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.084729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059979 restraints weight = 46636.406| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.79 r_work: 0.2796 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19822 Z= 0.141 Angle : 0.524 9.960 28976 Z= 0.295 Chirality : 0.036 0.233 3613 Planarity : 0.004 0.045 1998 Dihedral : 21.886 173.850 8376 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 4.01 % Allowed : 25.35 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1095 helix: 1.17 (0.24), residues: 500 sheet: 0.82 (0.42), residues: 159 loop : -0.00 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 89 TYR 0.019 0.001 TYR I 6 PHE 0.009 0.001 PHE B 90 TRP 0.012 0.001 TRP C 201 HIS 0.003 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (19821) covalent geometry : angle 0.52412 / 0.30 (28976) hydrogen bonds : bond 0.04724 / 5.28 ( 785) hydrogen bonds : angle 3.76942 / 4.87 ( 1800) metal coordination : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7958 (t0) REVERT: G 15 ASP cc_start: 0.6523 (t70) cc_final: 0.6291 (t0) REVERT: G 21 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: G 75 VAL cc_start: 0.5734 (OUTLIER) cc_final: 0.5432 (t) REVERT: G 111 ARG cc_start: 0.7429 (tpt170) cc_final: 0.6626 (tpp80) REVERT: G 139 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6781 (pp20) REVERT: I 42 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7863 (tp30) REVERT: M 27 LYS cc_start: 0.8820 (tptm) cc_final: 0.8466 (tppp) REVERT: M 44 LYS cc_start: 0.9092 (mttt) cc_final: 0.8442 (mtpt) REVERT: M 50 GLU cc_start: 0.8163 (tp30) cc_final: 0.7736 (tp30) REVERT: N 6 MET cc_start: 0.9279 (mmm) cc_final: 0.8942 (mmm) REVERT: B 10 LEU cc_start: 0.5172 (mt) cc_final: 0.4525 (pp) REVERT: B 70 VAL cc_start: 0.6257 (t) cc_final: 0.6043 (t) REVERT: B 100 MET cc_start: 0.7355 (mtp) cc_final: 0.7000 (mtt) REVERT: B 114 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7126 (pp) REVERT: B 133 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6404 (mt-10) REVERT: B 154 MET cc_start: 0.6241 (ttp) cc_final: 0.5940 (mtt) outliers start: 37 outliers final: 22 residues processed: 219 average time/residue: 0.5890 time to fit residues: 145.6979 Evaluate side-chains 220 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 3 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 32 GLN I 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.084778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.060054 restraints weight = 46488.866| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.80 r_work: 0.2798 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19822 Z= 0.140 Angle : 0.533 11.434 28976 Z= 0.298 Chirality : 0.036 0.226 3613 Planarity : 0.004 0.032 1998 Dihedral : 21.870 174.353 8376 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 3.36 % Allowed : 25.68 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1095 helix: 1.09 (0.23), residues: 502 sheet: 0.83 (0.42), residues: 159 loop : 0.06 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.010 0.001 TYR B 213 PHE 0.009 0.001 PHE I 20 TRP 0.012 0.001 TRP C 201 HIS 0.003 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (19821) covalent geometry : angle 0.53285 / 0.30 (28976) hydrogen bonds : bond 0.04698 / 5.24 ( 785) hydrogen bonds : angle 3.77348 / 4.88 ( 1800) metal coordination : bond 0.00052 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7953 (t0) REVERT: G 15 ASP cc_start: 0.6475 (t70) cc_final: 0.6259 (t0) REVERT: G 21 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: G 56 LYS cc_start: 0.7374 (tmtt) cc_final: 0.7039 (tmmt) REVERT: G 75 VAL cc_start: 0.5627 (OUTLIER) cc_final: 0.5318 (t) REVERT: G 111 ARG cc_start: 0.7403 (tpt170) cc_final: 0.6608 (tpp80) REVERT: G 137 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7585 (ttpt) REVERT: G 139 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6780 (pp20) REVERT: I 42 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7907 (tp30) REVERT: J 47 GLU cc_start: 0.8885 (tt0) cc_final: 0.8657 (tt0) REVERT: M 27 LYS cc_start: 0.8841 (tptm) cc_final: 0.8482 (tppp) REVERT: M 44 LYS cc_start: 0.9104 (mttt) cc_final: 0.8457 (mtpt) REVERT: M 50 GLU cc_start: 0.8197 (tp30) cc_final: 0.7756 (tp30) REVERT: N 6 MET cc_start: 0.9275 (mmm) cc_final: 0.8939 (mmm) REVERT: N 54 ASP cc_start: 0.8945 (m-30) cc_final: 0.8685 (t0) REVERT: B 10 LEU cc_start: 0.5042 (mt) cc_final: 0.4443 (pp) REVERT: B 70 VAL cc_start: 0.6327 (t) cc_final: 0.6115 (t) REVERT: B 100 MET cc_start: 0.7379 (mtp) cc_final: 0.7030 (mtt) REVERT: B 114 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7047 (pp) REVERT: B 133 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6380 (tt0) REVERT: B 142 GLU cc_start: 0.7937 (pp20) cc_final: 0.7646 (pp20) REVERT: B 145 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7920 (pp20) REVERT: B 154 MET cc_start: 0.6420 (ttp) cc_final: 0.6120 (mtt) outliers start: 31 outliers final: 19 residues processed: 213 average time/residue: 0.6125 time to fit residues: 146.7959 Evaluate side-chains 214 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 126 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 32 GLN I 110 GLN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.083216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.058398 restraints weight = 46577.948| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.74 r_work: 0.2750 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19822 Z= 0.227 Angle : 0.603 9.968 28976 Z= 0.329 Chirality : 0.041 0.233 3613 Planarity : 0.005 0.038 1998 Dihedral : 21.810 175.517 8376 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 3.47 % Allowed : 26.00 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1095 helix: 1.03 (0.23), residues: 502 sheet: 0.86 (0.41), residues: 158 loop : -0.07 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 89 TYR 0.025 0.002 TYR I 6 PHE 0.013 0.001 PHE I 20 TRP 0.010 0.001 TRP B 23 HIS 0.010 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.23 (19821) covalent geometry : angle 0.60268 / 0.33 (28976) hydrogen bonds : bond 0.05057 / 5.56 ( 785) hydrogen bonds : angle 3.83522 / 4.98 ( 1800) metal coordination : bond 0.00124 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6903.08 seconds wall clock time: 118 minutes 26.44 seconds (7106.44 seconds total)