Starting phenix.real_space_refine on Sat Sep 12 21:56:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afn_11771/09_2026/7afn_11771_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afn_11771/09_2026/7afn_11771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7afn_11771/09_2026/7afn_11771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afn_11771/09_2026/7afn_11771.map" model { file = "/net/cci-nas-00/data/ceres_data/7afn_11771/09_2026/7afn_11771_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afn_11771/09_2026/7afn_11771_neut.cif" } resolution = 3.86 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= 0.003 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 11 5.21 5 S 28 5.16 5 C 9845 2.51 5 N 3449 2.21 5 O 4730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18520 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': 36, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 171} Link IDs: {'rna2p': 70, 'rna3p': 385} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 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: "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: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} 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: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 3.43, per 1000 atoms: 0.19 Number of scatterers: 18520 At special positions: 0 Unit cell: (121.52, 146.475, 125.86, 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 11 11.99 O 4730 8.00 N 3449 7.00 C 9845 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: 1.43 Conformation dependent library (CDL) restraints added in 384.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 9 sheets defined 49.7% alpha, 14.1% beta 146 base pairs and 207 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... 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 86 Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.653A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) 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 helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 25 through 51 removed outlier: 4.288A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 35 through 54 removed outlier: 3.541A pdb=" N SER G 41 " --> pdb=" O SER G 37 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.303A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU G 66 " --> pdb=" O PHE G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 106 removed outlier: 3.664A pdb=" N ARG G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 110 Processing helix chain 'G' and resid 115 through 129 removed outlier: 3.537A pdb=" N ARG G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 140 Processing helix chain 'G' and resid 140 through 148 removed outlier: 4.629A pdb=" N GLU G 146 " --> pdb=" O HIS G 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 56 removed outlier: 3.855A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 57 through 59 No H-bonds generated for 'chain 'I' and resid 57 through 59' Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 93 through 102 removed outlier: 4.446A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.710A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 62 Processing helix chain 'M' and resid 65 through 83 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 20 removed outlier: 3.849A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 39 through 51 removed outlier: 3.705A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 4.004A 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 Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'S' and resid 12 through 25 Processing helix chain 'S' and resid 70 through 75 removed outlier: 4.323A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 70 through 75' Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.567A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.721A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.489A 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) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 58 removed outlier: 6.617A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 166 through 171 removed outlier: 6.674A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 12 removed outlier: 6.119A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 40 through 41 Processing sheet with id=AA8, first strand: chain 'J' and resid 45 through 52 Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.326A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 578 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 207 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2050 1.31 - 1.43: 7783 1.43 - 1.56: 9000 1.56 - 1.69: 914 1.69 - 1.82: 54 Bond restraints: 19801 Sorted by residual: bond pdb=" O3' G 1 963 " pdb=" P A 1 964 " ideal model delta sigma weight residual 1.607 1.738 -0.131 1.20e-02 6.94e+03 1.18e+02 bond pdb=" N9 A 11188 " pdb=" C4 A 11188 " ideal model delta sigma weight residual 1.374 1.344 0.030 6.00e-03 2.78e+04 2.43e+01 bond pdb=" N PHE S 41 " pdb=" CA PHE S 41 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.03e+01 bond pdb=" CA ALA S 75 " pdb=" C ALA S 75 " ideal model delta sigma weight residual 1.524 1.572 -0.048 1.08e-02 8.57e+03 1.98e+01 bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.467 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 27239 2.23 - 4.46: 1592 4.46 - 6.69: 97 6.69 - 8.92: 15 8.92 - 11.15: 6 Bond angle restraints: 28949 Sorted by residual: angle pdb=" C3' G 1 963 " pdb=" O3' G 1 963 " pdb=" P A 1 964 " ideal model delta sigma weight residual 119.70 108.55 11.15 1.20e+00 6.94e-01 8.64e+01 angle pdb=" O2 C 11210 " pdb=" C2 C 11210 " pdb=" N3 C 11210 " ideal model delta sigma weight residual 121.90 116.42 5.48 7.00e-01 2.04e+00 6.13e+01 angle pdb=" N ARG S 55 " pdb=" CA ARG S 55 " pdb=" C ARG S 55 " ideal model delta sigma weight residual 113.97 106.22 7.75 1.28e+00 6.10e-01 3.67e+01 angle pdb=" O4' A 11188 " pdb=" C1' A 11188 " pdb=" N9 A 11188 " ideal model delta sigma weight residual 108.50 104.38 4.12 7.00e-01 2.04e+00 3.46e+01 angle pdb=" O5' A 1 964 " pdb=" C5' A 1 964 " pdb=" C4' A 1 964 " ideal model delta sigma weight residual 109.40 114.05 -4.65 8.00e-01 1.56e+00 3.38e+01 ... (remaining 28944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 11218 35.18 - 70.35: 1261 70.35 - 105.53: 157 105.53 - 140.70: 11 140.70 - 175.88: 4 Dihedral angle restraints: 12651 sinusoidal: 9481 harmonic: 3170 Sorted by residual: dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual -160.00 5.09 -165.09 1 1.50e+01 4.44e-03 8.39e+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 59.96 140.04 1 1.50e+01 4.44e-03 7.54e+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 232.00 56.12 175.88 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3338 0.119 - 0.237: 255 0.237 - 0.355: 15 0.355 - 0.474: 0 0.474 - 0.592: 1 Chirality restraints: 3609 Sorted by residual: chirality pdb=" CA ASN M 105 " pdb=" N ASN M 105 " pdb=" C ASN M 105 " pdb=" CB ASN M 105 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.77e+00 chirality pdb=" CA ILE C 68 " pdb=" N ILE C 68 " pdb=" C ILE C 68 " pdb=" CB ILE C 68 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C3' A 1 964 " pdb=" C4' A 1 964 " pdb=" O3' A 1 964 " pdb=" C2' A 1 964 " both_signs ideal model delta sigma weight residual False -2.48 -2.80 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 3606 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 1 966 " 0.018 2.00e-02 2.50e+03 2.71e-02 2.39e+01 pdb=" N9 2MG 1 966 " 0.002 2.00e-02 2.50e+03 pdb=" C8 2MG 1 966 " -0.014 2.00e-02 2.50e+03 pdb=" N7 2MG 1 966 " -0.019 2.00e-02 2.50e+03 pdb=" C5 2MG 1 966 " -0.005 2.00e-02 2.50e+03 pdb=" C6 2MG 1 966 " -0.000 2.00e-02 2.50e+03 pdb=" O6 2MG 1 966 " -0.015 2.00e-02 2.50e+03 pdb=" N1 2MG 1 966 " 0.014 2.00e-02 2.50e+03 pdb=" C2 2MG 1 966 " 0.026 2.00e-02 2.50e+03 pdb=" N2 2MG 1 966 " 0.039 2.00e-02 2.50e+03 pdb=" N3 2MG 1 966 " 0.023 2.00e-02 2.50e+03 pdb=" C4 2MG 1 966 " 0.007 2.00e-02 2.50e+03 pdb=" CM2 2MG 1 966 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 59 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO C 60 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 189 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C ALA C 189 " 0.069 2.00e-02 2.50e+03 pdb=" O ALA C 189 " -0.026 2.00e-02 2.50e+03 pdb=" N HIS C 190 " -0.023 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 149 2.38 - 3.01: 11542 3.01 - 3.64: 37141 3.64 - 4.27: 54017 4.27 - 4.90: 74306 Nonbonded interactions: 177155 Sorted by model distance: nonbonded pdb=" O5' C 11366 " pdb="MG MG 11606 " model vdw 1.755 2.170 nonbonded pdb=" O2' G 11242 " pdb="MG MG 11610 " model vdw 1.810 2.170 nonbonded pdb=" O3' G 11242 " pdb="MG MG 11610 " model vdw 1.823 2.170 nonbonded pdb=" O5' A 11238 " pdb="MG MG 11611 " model vdw 1.825 2.170 nonbonded pdb=" OP2 A 11238 " pdb="MG MG 11611 " model vdw 1.856 2.170 ... (remaining 177150 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 19.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.008 0.152 19802 Z= 0.724 Angle : 1.059 11.153 28949 Z= 0.859 Chirality : 0.068 0.592 3609 Planarity : 0.006 0.101 1995 Dihedral : 23.442 175.877 10599 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % 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: -1.93 (0.25), residues: 1092 helix: -0.85 (0.24), residues: 487 sheet: -1.11 (0.39), residues: 160 loop : -1.69 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 138 TYR 0.016 0.002 TYR M 23 PHE 0.025 0.002 PHE S 74 TRP 0.011 0.002 TRP N 101 HIS 0.005 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00838 / 0.72 (19801) covalent geometry : angle 1.05881 / 0.86 (28949) hydrogen bonds : bond 0.18020 / 20.04 ( 798) hydrogen bonds : angle 7.52815 / 9.89 ( 1823) metal coordination : bond 0.15162 / 7.58 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 MET cc_start: 0.9303 (mmm) cc_final: 0.8895 (tpp) REVERT: C 153 VAL cc_start: 0.9634 (m) cc_final: 0.9371 (m) REVERT: C 170 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8324 (tm-30) REVERT: C 183 ASP cc_start: 0.8491 (t0) cc_final: 0.8256 (t0) REVERT: G 31 MET cc_start: 0.8782 (ttp) cc_final: 0.8413 (ttp) REVERT: G 38 THR cc_start: 0.9231 (t) cc_final: 0.9029 (t) REVERT: I 7 TYR cc_start: 0.7518 (p90) cc_final: 0.7303 (p90) REVERT: I 111 VAL cc_start: 0.9203 (t) cc_final: 0.8534 (p) REVERT: J 10 LEU cc_start: 0.9605 (mt) cc_final: 0.9395 (mm) REVERT: J 19 ASP cc_start: 0.9221 (m-30) cc_final: 0.8884 (m-30) REVERT: J 49 PHE cc_start: 0.9355 (m-80) cc_final: 0.9075 (m-80) REVERT: J 63 ASP cc_start: 0.9308 (t0) cc_final: 0.8815 (t0) REVERT: J 64 GLN cc_start: 0.9361 (mt0) cc_final: 0.9124 (tp-100) REVERT: M 23 TYR cc_start: 0.8794 (t80) cc_final: 0.8296 (t80) REVERT: M 75 MET cc_start: 0.9398 (mmp) cc_final: 0.9181 (mmm) REVERT: M 78 LYS cc_start: 0.9383 (tptp) cc_final: 0.8378 (tptp) REVERT: N 89 MET cc_start: 0.9440 (mmp) cc_final: 0.9161 (mmm) REVERT: S 66 MET cc_start: 0.9245 (mtp) cc_final: 0.8707 (mtp) REVERT: S 73 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8360 (pt0) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1631 time to fit residues: 66.3494 Evaluate side-chains 145 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS C 32 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN J 4 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.028551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.022636 restraints weight = 221826.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.023381 restraints weight = 98057.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.023814 restraints weight = 59918.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.024130 restraints weight = 44857.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.024321 restraints weight = 37448.396| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19802 Z= 0.184 Angle : 0.691 8.679 28949 Z= 0.386 Chirality : 0.044 0.288 3609 Planarity : 0.006 0.064 1995 Dihedral : 24.178 171.164 8374 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.04 % Allowed : 18.13 % Favored : 78.83 % 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: -1.21 (0.24), residues: 1092 helix: -0.41 (0.22), residues: 507 sheet: -0.77 (0.40), residues: 164 loop : -1.11 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 72 TYR 0.036 0.002 TYR C 42 PHE 0.028 0.003 PHE B 126 TRP 0.014 0.001 TRP C 201 HIS 0.018 0.002 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (19801) covalent geometry : angle 0.69106 / 0.39 (28949) hydrogen bonds : bond 0.09080 / 10.35 ( 798) hydrogen bonds : angle 5.23252 / 6.79 ( 1823) metal coordination : bond 0.01170 / 0.58 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 PHE cc_start: 0.8345 (p90) cc_final: 0.8045 (p90) REVERT: B 122 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 100 GLN cc_start: 0.7830 (tm-30) cc_final: 0.5652 (tm-30) REVERT: C 129 MET cc_start: 0.9294 (mmm) cc_final: 0.8831 (tpp) REVERT: C 134 MET cc_start: 0.9622 (ptp) cc_final: 0.9194 (ppp) REVERT: C 142 MET cc_start: 0.9354 (mmm) cc_final: 0.8564 (mmm) REVERT: C 170 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8688 (tm-30) REVERT: C 183 ASP cc_start: 0.8483 (t0) cc_final: 0.8226 (t0) REVERT: G 31 MET cc_start: 0.8895 (ttp) cc_final: 0.8415 (ttp) REVERT: G 38 THR cc_start: 0.9193 (t) cc_final: 0.8903 (t) REVERT: I 112 GLU cc_start: 0.8752 (tp30) cc_final: 0.8266 (tp30) REVERT: I 115 LYS cc_start: 0.9358 (mttt) cc_final: 0.8897 (mmtp) REVERT: J 19 ASP cc_start: 0.9204 (m-30) cc_final: 0.8963 (m-30) REVERT: J 46 LYS cc_start: 0.9379 (mptt) cc_final: 0.9131 (mmtm) REVERT: J 63 ASP cc_start: 0.9354 (t0) cc_final: 0.8944 (t0) REVERT: M 23 TYR cc_start: 0.8818 (t80) cc_final: 0.8430 (t80) REVERT: M 78 LYS cc_start: 0.9371 (tptp) cc_final: 0.9044 (tppt) REVERT: M 81 MET cc_start: 0.8849 (ppp) cc_final: 0.8139 (ppp) REVERT: N 82 ILE cc_start: 0.9370 (mt) cc_final: 0.8748 (mm) REVERT: N 89 MET cc_start: 0.9384 (mmp) cc_final: 0.8899 (mmt) REVERT: S 41 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8784 (m-80) REVERT: S 66 MET cc_start: 0.9356 (mtp) cc_final: 0.8900 (mtp) outliers start: 28 outliers final: 13 residues processed: 177 average time/residue: 0.1237 time to fit residues: 34.2239 Evaluate side-chains 148 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain S residue 41 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 120 optimal weight: 0.0970 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 177 ASN B 227 GLN ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS ** N 49 GLN ** 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 = 0.2797 r_free = 0.2797 target = 0.027532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.021690 restraints weight = 228295.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.022428 restraints weight = 99696.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.022848 restraints weight = 60520.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.023153 restraints weight = 45193.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.023274 restraints weight = 37552.844| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19802 Z= 0.217 Angle : 0.637 8.279 28949 Z= 0.355 Chirality : 0.041 0.268 3609 Planarity : 0.005 0.051 1995 Dihedral : 24.044 176.115 8374 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.69 % Allowed : 20.30 % Favored : 76.00 % 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 (0.24), residues: 1092 helix: -0.07 (0.22), residues: 502 sheet: -0.89 (0.39), residues: 163 loop : -0.99 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 111 TYR 0.022 0.002 TYR C 42 PHE 0.046 0.003 PHE B 16 TRP 0.011 0.002 TRP C 201 HIS 0.010 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.22 (19801) covalent geometry : angle 0.63665 / 0.36 (28949) hydrogen bonds : bond 0.08887 / 10.12 ( 798) hydrogen bonds : angle 4.94375 / 6.51 ( 1823) metal coordination : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8429 (tm-30) REVERT: C 129 MET cc_start: 0.9243 (mmm) cc_final: 0.8790 (tpp) REVERT: C 134 MET cc_start: 0.9646 (ptp) cc_final: 0.9233 (ppp) REVERT: C 142 MET cc_start: 0.9389 (mmm) cc_final: 0.8601 (mmp) REVERT: C 170 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8655 (tm-30) REVERT: C 183 ASP cc_start: 0.8619 (t0) cc_final: 0.8389 (t0) REVERT: G 31 MET cc_start: 0.8843 (ttp) cc_final: 0.8305 (ttp) REVERT: G 38 THR cc_start: 0.9374 (t) cc_final: 0.9127 (t) REVERT: G 71 PRO cc_start: 0.9113 (Cg_exo) cc_final: 0.8826 (Cg_endo) REVERT: I 42 GLU cc_start: 0.8735 (pp20) cc_final: 0.8222 (pp20) REVERT: I 46 MET cc_start: 0.9089 (mmm) cc_final: 0.8517 (mmm) REVERT: I 57 MET cc_start: 0.9435 (tpp) cc_final: 0.8936 (tmm) REVERT: I 65 ILE cc_start: 0.9522 (pt) cc_final: 0.9109 (mm) REVERT: I 112 GLU cc_start: 0.8739 (tp30) cc_final: 0.8285 (tp30) REVERT: I 115 LYS cc_start: 0.9300 (mttt) cc_final: 0.8920 (mmtp) REVERT: J 19 ASP cc_start: 0.9254 (m-30) cc_final: 0.9027 (m-30) REVERT: J 63 ASP cc_start: 0.9217 (t0) cc_final: 0.8801 (t70) REVERT: M 23 TYR cc_start: 0.8871 (t80) cc_final: 0.8323 (t80) REVERT: M 27 LYS cc_start: 0.9625 (tptt) cc_final: 0.9158 (tppt) REVERT: M 31 LYS cc_start: 0.9508 (pttp) cc_final: 0.9193 (mtmm) REVERT: M 78 LYS cc_start: 0.9340 (tptp) cc_final: 0.8818 (tptp) REVERT: N 89 MET cc_start: 0.9410 (mmp) cc_final: 0.8952 (mmt) REVERT: S 41 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8684 (m-80) REVERT: S 66 MET cc_start: 0.9355 (mtp) cc_final: 0.8873 (mtp) outliers start: 34 outliers final: 20 residues processed: 162 average time/residue: 0.1322 time to fit residues: 33.2405 Evaluate side-chains 146 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 41 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 139 optimal weight: 0.6980 chunk 25 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 178 ASN G 52 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** N 49 GLN ** 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 = 0.2811 r_free = 0.2811 target = 0.027888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.022014 restraints weight = 222684.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.022738 restraints weight = 97860.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.023174 restraints weight = 59425.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.023482 restraints weight = 44170.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.023644 restraints weight = 36804.426| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19802 Z= 0.146 Angle : 0.590 9.685 28949 Z= 0.332 Chirality : 0.039 0.342 3609 Planarity : 0.005 0.048 1995 Dihedral : 23.922 179.516 8374 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.47 % Allowed : 21.28 % Favored : 75.24 % 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: -0.74 (0.24), residues: 1092 helix: 0.12 (0.22), residues: 511 sheet: -0.62 (0.39), residues: 162 loop : -1.04 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 111 TYR 0.025 0.002 TYR C 168 PHE 0.013 0.002 PHE N 77 TRP 0.049 0.002 TRP G 103 HIS 0.008 0.001 HIS M 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (19801) covalent geometry : angle 0.59045 / 0.33 (28949) hydrogen bonds : bond 0.07304 / 8.19 ( 798) hydrogen bonds : angle 4.72682 / 6.21 ( 1823) metal coordination : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8505 (tm-30) REVERT: C 25 ASN cc_start: 0.9369 (m-40) cc_final: 0.9094 (m-40) REVERT: C 129 MET cc_start: 0.9256 (mmm) cc_final: 0.8829 (tpp) REVERT: C 134 MET cc_start: 0.9640 (ptp) cc_final: 0.9186 (ppp) REVERT: C 142 MET cc_start: 0.9415 (mmm) cc_final: 0.8542 (mmp) REVERT: C 170 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8671 (tm-30) REVERT: C 183 ASP cc_start: 0.8550 (t0) cc_final: 0.8281 (t0) REVERT: C 211 MET cc_start: 0.8340 (mmm) cc_final: 0.8027 (mmm) REVERT: G 29 ILE cc_start: 0.9590 (mm) cc_final: 0.9302 (tt) REVERT: G 31 MET cc_start: 0.8896 (ttp) cc_final: 0.8273 (ttp) REVERT: G 38 THR cc_start: 0.9413 (t) cc_final: 0.9170 (t) REVERT: G 103 TRP cc_start: 0.9684 (m-10) cc_final: 0.9339 (m100) REVERT: I 42 GLU cc_start: 0.8768 (pp20) cc_final: 0.8235 (pp20) REVERT: I 46 MET cc_start: 0.9141 (mmm) cc_final: 0.8539 (mmm) REVERT: I 57 MET cc_start: 0.9418 (tpp) cc_final: 0.9160 (tpp) REVERT: I 65 ILE cc_start: 0.9539 (pt) cc_final: 0.9173 (mm) REVERT: I 112 GLU cc_start: 0.8763 (tp30) cc_final: 0.8373 (tp30) REVERT: I 115 LYS cc_start: 0.9254 (mttt) cc_final: 0.8866 (mmtp) REVERT: I 118 LEU cc_start: 0.9567 (mm) cc_final: 0.9082 (tp) REVERT: J 44 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8986 (t) REVERT: J 63 ASP cc_start: 0.9238 (t0) cc_final: 0.8835 (t70) REVERT: M 23 TYR cc_start: 0.8548 (t80) cc_final: 0.8201 (t80) REVERT: M 27 LYS cc_start: 0.9554 (tptt) cc_final: 0.8989 (tppt) REVERT: M 31 LYS cc_start: 0.9451 (pttp) cc_final: 0.9131 (pttp) REVERT: M 78 LYS cc_start: 0.9405 (tptp) cc_final: 0.9063 (tptm) REVERT: N 89 MET cc_start: 0.9456 (mmp) cc_final: 0.9004 (mmt) REVERT: S 66 MET cc_start: 0.9315 (mtp) cc_final: 0.8822 (mtp) outliers start: 32 outliers final: 19 residues processed: 169 average time/residue: 0.1176 time to fit residues: 31.4981 Evaluate side-chains 151 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain S residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 101 optimal weight: 0.0980 chunk 114 optimal weight: 0.0470 chunk 79 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.6284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 52 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.027959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.022174 restraints weight = 221872.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.022906 restraints weight = 98104.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.023357 restraints weight = 59619.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.023669 restraints weight = 44251.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.023841 restraints weight = 36624.591| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19802 Z= 0.136 Angle : 0.568 8.112 28949 Z= 0.320 Chirality : 0.037 0.264 3609 Planarity : 0.005 0.046 1995 Dihedral : 23.782 178.414 8374 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.47 % Allowed : 22.04 % Favored : 74.48 % 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: -0.51 (0.24), residues: 1092 helix: 0.30 (0.22), residues: 511 sheet: -0.62 (0.40), residues: 158 loop : -0.87 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 95 TYR 0.026 0.002 TYR C 168 PHE 0.041 0.002 PHE B 16 TRP 0.024 0.001 TRP G 103 HIS 0.005 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (19801) covalent geometry : angle 0.56843 / 0.32 (28949) hydrogen bonds : bond 0.06858 / 7.73 ( 798) hydrogen bonds : angle 4.56830 / 5.99 ( 1823) metal coordination : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8587 (tm-30) REVERT: B 146 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.8901 (p0) REVERT: C 25 ASN cc_start: 0.9345 (m-40) cc_final: 0.9058 (m-40) REVERT: C 129 MET cc_start: 0.9211 (mmm) cc_final: 0.8790 (tpp) REVERT: C 134 MET cc_start: 0.9626 (ptp) cc_final: 0.9185 (ppp) REVERT: C 142 MET cc_start: 0.9404 (mmm) cc_final: 0.8564 (mmp) REVERT: C 170 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8694 (tm-30) REVERT: C 183 ASP cc_start: 0.8609 (t0) cc_final: 0.8315 (t0) REVERT: C 211 MET cc_start: 0.8419 (mmm) cc_final: 0.7826 (mmm) REVERT: G 29 ILE cc_start: 0.9634 (mm) cc_final: 0.9348 (tt) REVERT: G 31 MET cc_start: 0.8886 (ttp) cc_final: 0.8236 (ttp) REVERT: G 38 THR cc_start: 0.9491 (t) cc_final: 0.9257 (t) REVERT: G 103 TRP cc_start: 0.9704 (m-10) cc_final: 0.9214 (m100) REVERT: I 42 GLU cc_start: 0.8767 (pp20) cc_final: 0.8255 (pp20) REVERT: I 46 MET cc_start: 0.9138 (mmm) cc_final: 0.8496 (mmm) REVERT: I 57 MET cc_start: 0.9416 (tpp) cc_final: 0.9180 (tpp) REVERT: I 65 ILE cc_start: 0.9492 (pt) cc_final: 0.9137 (mm) REVERT: I 112 GLU cc_start: 0.8706 (tp30) cc_final: 0.8282 (tp30) REVERT: I 115 LYS cc_start: 0.9275 (mttt) cc_final: 0.8897 (mmtp) REVERT: I 118 LEU cc_start: 0.9575 (mm) cc_final: 0.9148 (tp) REVERT: J 63 ASP cc_start: 0.9267 (t0) cc_final: 0.8838 (t70) REVERT: J 66 GLU cc_start: 0.8572 (tp30) cc_final: 0.8312 (tm-30) REVERT: M 78 LYS cc_start: 0.9345 (tptp) cc_final: 0.9072 (tptm) REVERT: N 6 MET cc_start: 0.8870 (mmt) cc_final: 0.8551 (mmp) REVERT: N 89 MET cc_start: 0.9429 (mmp) cc_final: 0.9063 (mmt) REVERT: S 66 MET cc_start: 0.9319 (mtp) cc_final: 0.8818 (mtp) outliers start: 32 outliers final: 23 residues processed: 159 average time/residue: 0.1280 time to fit residues: 31.8724 Evaluate side-chains 153 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 95 optimal weight: 8.9990 chunk 133 optimal weight: 0.0010 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 148 optimal weight: 0.0060 chunk 39 optimal weight: 20.0000 overall best weight: 2.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 102 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.027679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.021855 restraints weight = 223921.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.022577 restraints weight = 97791.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.023016 restraints weight = 59564.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.023307 restraints weight = 44838.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.023476 restraints weight = 37450.168| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19802 Z= 0.153 Angle : 0.565 8.073 28949 Z= 0.317 Chirality : 0.037 0.265 3609 Planarity : 0.005 0.046 1995 Dihedral : 23.713 178.682 8374 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.47 % Allowed : 23.24 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 1092 helix: 0.51 (0.22), residues: 506 sheet: -0.57 (0.40), residues: 158 loop : -0.68 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 95 TYR 0.027 0.002 TYR C 168 PHE 0.015 0.002 PHE S 41 TRP 0.014 0.001 TRP G 103 HIS 0.006 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (19801) covalent geometry : angle 0.56509 / 0.32 (28949) hydrogen bonds : bond 0.06921 / 7.82 ( 798) hydrogen bonds : angle 4.56413 / 5.99 ( 1823) metal coordination : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.4978 (mtp) REVERT: B 146 ASN cc_start: 0.9431 (OUTLIER) cc_final: 0.8939 (p0) REVERT: C 25 ASN cc_start: 0.9334 (m-40) cc_final: 0.9053 (m-40) REVERT: C 129 MET cc_start: 0.9247 (mmm) cc_final: 0.8786 (tpp) REVERT: C 134 MET cc_start: 0.9637 (ptp) cc_final: 0.9205 (ppp) REVERT: C 142 MET cc_start: 0.9365 (mmm) cc_final: 0.8542 (mmp) REVERT: C 170 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8733 (tm-30) REVERT: C 183 ASP cc_start: 0.8629 (t0) cc_final: 0.8309 (t0) REVERT: C 211 MET cc_start: 0.8345 (mmm) cc_final: 0.7795 (mmm) REVERT: G 29 ILE cc_start: 0.9651 (mm) cc_final: 0.9334 (tt) REVERT: G 31 MET cc_start: 0.8886 (ttp) cc_final: 0.8247 (ttp) REVERT: G 38 THR cc_start: 0.9507 (t) cc_final: 0.9284 (t) REVERT: G 95 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8842 (tpt170) REVERT: G 103 TRP cc_start: 0.9686 (m-10) cc_final: 0.9220 (m100) REVERT: I 42 GLU cc_start: 0.8779 (pp20) cc_final: 0.8255 (pp20) REVERT: I 46 MET cc_start: 0.9170 (mmm) cc_final: 0.8548 (mmm) REVERT: I 57 MET cc_start: 0.9385 (tpp) cc_final: 0.9020 (tpp) REVERT: I 65 ILE cc_start: 0.9519 (pt) cc_final: 0.9105 (mm) REVERT: I 112 GLU cc_start: 0.8720 (tp30) cc_final: 0.8325 (tp30) REVERT: I 115 LYS cc_start: 0.9240 (mttt) cc_final: 0.8871 (mmtp) REVERT: I 118 LEU cc_start: 0.9528 (mm) cc_final: 0.8866 (tp) REVERT: J 44 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9041 (t) REVERT: J 63 ASP cc_start: 0.9217 (t0) cc_final: 0.8827 (t70) REVERT: J 66 GLU cc_start: 0.8612 (tp30) cc_final: 0.7916 (tm-30) REVERT: M 27 LYS cc_start: 0.9451 (tptt) cc_final: 0.9164 (tppt) REVERT: M 78 LYS cc_start: 0.9349 (tptp) cc_final: 0.9087 (tptm) REVERT: N 6 MET cc_start: 0.8857 (mmt) cc_final: 0.8535 (mmp) REVERT: N 89 MET cc_start: 0.9440 (mmp) cc_final: 0.9093 (mmt) REVERT: S 66 MET cc_start: 0.9330 (mtp) cc_final: 0.8923 (mtp) outliers start: 32 outliers final: 20 residues processed: 154 average time/residue: 0.1449 time to fit residues: 34.1495 Evaluate side-chains 152 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 45 optimal weight: 10.0000 chunk 148 optimal weight: 0.0170 chunk 126 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 102 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.027336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.021639 restraints weight = 226466.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.022349 restraints weight = 98690.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.022761 restraints weight = 60145.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.023062 restraints weight = 45147.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.023237 restraints weight = 37636.815| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19802 Z= 0.178 Angle : 0.583 9.683 28949 Z= 0.324 Chirality : 0.038 0.265 3609 Planarity : 0.005 0.043 1995 Dihedral : 23.695 179.024 8374 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.58 % Allowed : 24.21 % Favored : 72.20 % 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: -0.34 (0.25), residues: 1092 helix: 0.46 (0.22), residues: 513 sheet: -0.68 (0.40), residues: 162 loop : -0.74 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 95 TYR 0.027 0.002 TYR C 168 PHE 0.017 0.002 PHE I 127 TRP 0.010 0.001 TRP C 201 HIS 0.006 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.18 (19801) covalent geometry : angle 0.58283 / 0.32 (28949) hydrogen bonds : bond 0.07196 / 8.14 ( 798) hydrogen bonds : angle 4.56372 / 5.96 ( 1823) metal coordination : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.5305 (OUTLIER) cc_final: 0.5085 (mtp) REVERT: B 146 ASN cc_start: 0.9458 (OUTLIER) cc_final: 0.8997 (p0) REVERT: C 25 ASN cc_start: 0.9335 (m-40) cc_final: 0.9073 (m-40) REVERT: C 129 MET cc_start: 0.9256 (mmm) cc_final: 0.8819 (tpp) REVERT: C 134 MET cc_start: 0.9624 (ptp) cc_final: 0.9203 (ppp) REVERT: C 142 MET cc_start: 0.9356 (mmm) cc_final: 0.8592 (mmp) REVERT: C 170 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8751 (tm-30) REVERT: C 183 ASP cc_start: 0.8632 (t0) cc_final: 0.8264 (t0) REVERT: C 211 MET cc_start: 0.8393 (mmm) cc_final: 0.7873 (mmm) REVERT: G 29 ILE cc_start: 0.9656 (mm) cc_final: 0.9338 (tt) REVERT: G 31 MET cc_start: 0.8931 (ttp) cc_final: 0.8241 (ttp) REVERT: G 38 THR cc_start: 0.9545 (t) cc_final: 0.9339 (t) REVERT: G 95 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8839 (tpt170) REVERT: G 103 TRP cc_start: 0.9681 (m-10) cc_final: 0.9199 (m100) REVERT: I 42 GLU cc_start: 0.8804 (pp20) cc_final: 0.8267 (pp20) REVERT: I 46 MET cc_start: 0.9203 (mmm) cc_final: 0.8524 (mmm) REVERT: I 57 MET cc_start: 0.9421 (tpp) cc_final: 0.9022 (tpp) REVERT: I 65 ILE cc_start: 0.9515 (pt) cc_final: 0.9093 (mm) REVERT: I 110 GLN cc_start: 0.8921 (mp10) cc_final: 0.8610 (pm20) REVERT: I 112 GLU cc_start: 0.8762 (tp30) cc_final: 0.8368 (tp30) REVERT: I 115 LYS cc_start: 0.9295 (mttt) cc_final: 0.8914 (mmtp) REVERT: I 118 LEU cc_start: 0.9501 (mm) cc_final: 0.9007 (tp) REVERT: J 44 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9041 (t) REVERT: J 63 ASP cc_start: 0.9238 (t0) cc_final: 0.8831 (t70) REVERT: J 66 GLU cc_start: 0.8595 (tp30) cc_final: 0.7996 (tm-30) REVERT: M 27 LYS cc_start: 0.9511 (tptt) cc_final: 0.9076 (tptp) REVERT: M 78 LYS cc_start: 0.9356 (tptp) cc_final: 0.9036 (tptp) REVERT: N 41 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8816 (ptp-110) REVERT: N 89 MET cc_start: 0.9455 (mmp) cc_final: 0.9109 (mmt) REVERT: S 66 MET cc_start: 0.9368 (mtp) cc_final: 0.8973 (mtp) outliers start: 33 outliers final: 23 residues processed: 149 average time/residue: 0.1413 time to fit residues: 32.7126 Evaluate side-chains 154 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 139 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 149 optimal weight: 0.0470 chunk 89 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 chunk 69 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.028269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.022380 restraints weight = 220431.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.023141 restraints weight = 95726.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.023587 restraints weight = 58138.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.023908 restraints weight = 43538.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.024057 restraints weight = 36281.734| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 19802 Z= 0.116 Angle : 0.564 10.192 28949 Z= 0.314 Chirality : 0.037 0.310 3609 Planarity : 0.004 0.048 1995 Dihedral : 23.606 176.966 8374 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.82 % Allowed : 25.62 % Favored : 71.55 % 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: -0.13 (0.25), residues: 1092 helix: 0.53 (0.23), residues: 510 sheet: -0.32 (0.41), residues: 159 loop : -0.60 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 102 TYR 0.025 0.002 TYR C 168 PHE 0.010 0.001 PHE B 90 TRP 0.015 0.002 TRP G 103 HIS 0.003 0.001 HIS J 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 (19801) covalent geometry : angle 0.56403 / 0.31 (28949) hydrogen bonds : bond 0.06077 / 6.86 ( 798) hydrogen bonds : angle 4.40921 / 5.70 ( 1823) metal coordination : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.5020 (mtp) REVERT: B 122 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8211 (pp30) REVERT: B 146 ASN cc_start: 0.9465 (m110) cc_final: 0.9010 (p0) REVERT: C 25 ASN cc_start: 0.9340 (m-40) cc_final: 0.9069 (m-40) REVERT: C 129 MET cc_start: 0.9237 (mmm) cc_final: 0.8799 (tpp) REVERT: C 134 MET cc_start: 0.9625 (ptp) cc_final: 0.9197 (ppp) REVERT: C 142 MET cc_start: 0.9353 (mmm) cc_final: 0.8473 (mmp) REVERT: C 170 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8766 (tm-30) REVERT: C 183 ASP cc_start: 0.8636 (t0) cc_final: 0.8218 (t0) REVERT: C 211 MET cc_start: 0.8330 (mmm) cc_final: 0.7832 (mmm) REVERT: G 29 ILE cc_start: 0.9660 (mm) cc_final: 0.9356 (tt) REVERT: G 31 MET cc_start: 0.8886 (ttp) cc_final: 0.8138 (ttp) REVERT: G 38 THR cc_start: 0.9545 (t) cc_final: 0.9331 (t) REVERT: G 103 TRP cc_start: 0.9664 (m-10) cc_final: 0.9321 (m100) REVERT: I 42 GLU cc_start: 0.8759 (pp20) cc_final: 0.8209 (pp20) REVERT: I 46 MET cc_start: 0.9208 (mmm) cc_final: 0.8500 (mmm) REVERT: I 65 ILE cc_start: 0.9531 (pt) cc_final: 0.9245 (mm) REVERT: I 110 GLN cc_start: 0.8926 (mp10) cc_final: 0.8682 (pm20) REVERT: I 112 GLU cc_start: 0.8704 (tp30) cc_final: 0.8306 (tp30) REVERT: I 115 LYS cc_start: 0.9259 (mttt) cc_final: 0.8909 (mmtp) REVERT: I 118 LEU cc_start: 0.9423 (mm) cc_final: 0.8919 (tp) REVERT: J 63 ASP cc_start: 0.9282 (t0) cc_final: 0.8838 (t70) REVERT: J 66 GLU cc_start: 0.8643 (tp30) cc_final: 0.7984 (tm-30) REVERT: M 27 LYS cc_start: 0.9480 (tptt) cc_final: 0.9122 (tptt) REVERT: M 31 LYS cc_start: 0.9479 (pttm) cc_final: 0.9252 (mtmm) REVERT: M 78 LYS cc_start: 0.9348 (tptp) cc_final: 0.9008 (tptp) REVERT: N 6 MET cc_start: 0.8820 (mmt) cc_final: 0.8554 (mmp) REVERT: N 89 MET cc_start: 0.9409 (mmp) cc_final: 0.8986 (mmt) REVERT: S 66 MET cc_start: 0.9325 (mtp) cc_final: 0.8935 (mtp) outliers start: 26 outliers final: 19 residues processed: 155 average time/residue: 0.1397 time to fit residues: 33.6848 Evaluate side-chains 149 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain S residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 75 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.027068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.021460 restraints weight = 229746.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.022172 restraints weight = 100414.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.022604 restraints weight = 60649.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.022886 restraints weight = 45295.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.023054 restraints weight = 37751.810| |-----------------------------------------------------------------------------| r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19802 Z= 0.215 Angle : 0.612 9.956 28949 Z= 0.337 Chirality : 0.039 0.270 3609 Planarity : 0.005 0.048 1995 Dihedral : 23.611 179.969 8374 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.15 % Allowed : 25.84 % Favored : 71.01 % 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: -0.14 (0.25), residues: 1092 helix: 0.49 (0.23), residues: 514 sheet: -0.39 (0.41), residues: 161 loop : -0.54 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 95 TYR 0.026 0.002 TYR C 168 PHE 0.017 0.002 PHE I 127 TRP 0.009 0.002 TRP S 34 HIS 0.006 0.002 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.22 (19801) covalent geometry : angle 0.61223 / 0.34 (28949) hydrogen bonds : bond 0.07704 / 8.76 ( 798) hydrogen bonds : angle 4.55739 / 5.91 ( 1823) metal coordination : bond 0.00069 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.5688 (OUTLIER) cc_final: 0.5382 (mtp) REVERT: C 25 ASN cc_start: 0.9329 (m-40) cc_final: 0.9057 (m-40) REVERT: C 129 MET cc_start: 0.9253 (mmm) cc_final: 0.8830 (tpp) REVERT: C 134 MET cc_start: 0.9582 (ptp) cc_final: 0.9174 (ppp) REVERT: C 142 MET cc_start: 0.9331 (mmm) cc_final: 0.8473 (mmp) REVERT: C 170 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8798 (tm-30) REVERT: C 183 ASP cc_start: 0.8634 (t0) cc_final: 0.8262 (t0) REVERT: G 29 ILE cc_start: 0.9643 (mm) cc_final: 0.9252 (tt) REVERT: G 31 MET cc_start: 0.8918 (ttp) cc_final: 0.8176 (ttp) REVERT: G 103 TRP cc_start: 0.9645 (m-10) cc_final: 0.9296 (m100) REVERT: I 42 GLU cc_start: 0.8850 (pp20) cc_final: 0.8289 (pp20) REVERT: I 46 MET cc_start: 0.9222 (mmm) cc_final: 0.8512 (mmm) REVERT: I 57 MET cc_start: 0.9383 (tpp) cc_final: 0.9182 (mmm) REVERT: I 65 ILE cc_start: 0.9484 (pt) cc_final: 0.9207 (mm) REVERT: I 115 LYS cc_start: 0.9294 (mttt) cc_final: 0.8893 (mmtp) REVERT: I 118 LEU cc_start: 0.9460 (mm) cc_final: 0.8946 (tp) REVERT: J 46 LYS cc_start: 0.9472 (mptt) cc_final: 0.9136 (mmmm) REVERT: J 63 ASP cc_start: 0.9235 (t0) cc_final: 0.8830 (t0) REVERT: J 66 GLU cc_start: 0.8658 (tp30) cc_final: 0.7148 (tp30) REVERT: M 27 LYS cc_start: 0.9480 (tptt) cc_final: 0.9013 (tptp) REVERT: M 78 LYS cc_start: 0.9371 (tptp) cc_final: 0.9052 (tptp) REVERT: N 6 MET cc_start: 0.8877 (mmt) cc_final: 0.8619 (mmp) REVERT: N 38 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8771 (p0) REVERT: N 89 MET cc_start: 0.9439 (mmp) cc_final: 0.9029 (mmt) REVERT: S 66 MET cc_start: 0.9354 (mtp) cc_final: 0.8936 (mtp) outliers start: 29 outliers final: 24 residues processed: 145 average time/residue: 0.1265 time to fit residues: 29.1813 Evaluate side-chains 152 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 143 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 142 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.027953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.022122 restraints weight = 222815.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.022866 restraints weight = 96349.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.023311 restraints weight = 58416.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.023598 restraints weight = 43976.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.023749 restraints weight = 36930.893| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 19802 Z= 0.123 Angle : 0.580 11.164 28949 Z= 0.322 Chirality : 0.036 0.273 3609 Planarity : 0.005 0.050 1995 Dihedral : 23.579 177.803 8374 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.28 % Allowed : 27.14 % Favored : 70.58 % 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: 1092 helix: 0.48 (0.23), residues: 516 sheet: -0.28 (0.42), residues: 159 loop : -0.47 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 111 TYR 0.023 0.002 TYR C 168 PHE 0.012 0.001 PHE B 90 TRP 0.024 0.002 TRP G 103 HIS 0.007 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (19801) covalent geometry : angle 0.58000 / 0.32 (28949) hydrogen bonds : bond 0.06188 / 7.05 ( 798) hydrogen bonds : angle 4.45174 / 5.73 ( 1823) metal coordination : bond 0.00028 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.5606 (mtp) REVERT: B 36 ASN cc_start: 0.7544 (m-40) cc_final: 0.7264 (p0) REVERT: B 122 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8163 (pp30) REVERT: B 146 ASN cc_start: 0.9531 (m110) cc_final: 0.9097 (p0) REVERT: C 25 ASN cc_start: 0.9316 (m-40) cc_final: 0.9042 (m-40) REVERT: C 129 MET cc_start: 0.9247 (mmm) cc_final: 0.8843 (tpp) REVERT: C 134 MET cc_start: 0.9606 (ptp) cc_final: 0.9184 (ppp) REVERT: C 142 MET cc_start: 0.9340 (mmm) cc_final: 0.8453 (mmp) REVERT: C 170 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8753 (tm-30) REVERT: C 183 ASP cc_start: 0.8619 (t0) cc_final: 0.8280 (t0) REVERT: G 29 ILE cc_start: 0.9613 (mm) cc_final: 0.9336 (tt) REVERT: G 31 MET cc_start: 0.8914 (ttp) cc_final: 0.8196 (ttp) REVERT: G 52 GLN cc_start: 0.9344 (mm110) cc_final: 0.9033 (pm20) REVERT: G 103 TRP cc_start: 0.9626 (m-10) cc_final: 0.9319 (m100) REVERT: I 42 GLU cc_start: 0.8750 (pp20) cc_final: 0.8141 (pp20) REVERT: I 46 MET cc_start: 0.9222 (mmm) cc_final: 0.8488 (mmm) REVERT: I 61 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9054 (mt) REVERT: I 65 ILE cc_start: 0.9544 (pt) cc_final: 0.9287 (mm) REVERT: I 112 GLU cc_start: 0.8820 (tp30) cc_final: 0.7823 (tp30) REVERT: I 118 LEU cc_start: 0.9450 (mm) cc_final: 0.8913 (tp) REVERT: J 63 ASP cc_start: 0.9240 (t0) cc_final: 0.8823 (t0) REVERT: M 27 LYS cc_start: 0.9468 (tptt) cc_final: 0.8929 (tptt) REVERT: M 31 LYS cc_start: 0.9501 (pttm) cc_final: 0.9111 (pttm) REVERT: M 78 LYS cc_start: 0.9356 (tptp) cc_final: 0.9087 (tptp) REVERT: N 6 MET cc_start: 0.8887 (mmt) cc_final: 0.8635 (mmp) REVERT: N 89 MET cc_start: 0.9416 (mmp) cc_final: 0.8987 (mmt) REVERT: S 66 MET cc_start: 0.9320 (mtp) cc_final: 0.8829 (mtp) outliers start: 21 outliers final: 18 residues processed: 144 average time/residue: 0.1437 time to fit residues: 32.5804 Evaluate side-chains 149 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain S residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 42 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 141 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.027990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.022143 restraints weight = 224272.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.022884 restraints weight = 97098.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.023300 restraints weight = 59131.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.023625 restraints weight = 44634.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.023758 restraints weight = 37590.155| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19802 Z= 0.126 Angle : 0.577 13.410 28949 Z= 0.318 Chirality : 0.036 0.288 3609 Planarity : 0.005 0.052 1995 Dihedral : 23.495 178.345 8374 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.71 % Allowed : 26.38 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.25), residues: 1092 helix: 0.55 (0.23), residues: 517 sheet: -0.23 (0.41), residues: 161 loop : -0.48 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 32 TYR 0.023 0.002 TYR C 168 PHE 0.022 0.001 PHE I 127 TRP 0.016 0.002 TRP G 103 HIS 0.005 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (19801) covalent geometry : angle 0.57707 / 0.32 (28949) hydrogen bonds : bond 0.06102 / 6.96 ( 798) hydrogen bonds : angle 4.42624 / 5.70 ( 1823) metal coordination : bond 0.00017 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2986.87 seconds wall clock time: 52 minutes 57.25 seconds (3177.25 seconds total)