Starting phenix.real_space_refine on Mon Apr 6 12:00:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afn_11771/04_2026/7afn_11771_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afn_11771/04_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_11771/04_2026/7afn_11771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afn_11771/04_2026/7afn_11771.map" model { file = "/net/cci-nas-00/data/ceres_data/7afn_11771/04_2026/7afn_11771_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afn_11771/04_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-2.1rc1-6017/lib/python3.9/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: 3.64, per 1000 atoms: 0.20 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: 1.28 Conformation dependent library (CDL) restraints added in 424.7 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: 3.05 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: 4.19 Time building geometry restraints manager: 1.83 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 1.50e-02 4.44e+03 7.57e+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 bond pdb=" C GLY C 81 " pdb=" O GLY C 81 " ideal model delta sigma weight residual 1.236 1.180 0.055 1.31e-02 5.83e+03 1.79e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 27519 2.33 - 4.66: 1334 4.66 - 6.99: 76 6.99 - 9.32: 16 9.32 - 11.65: 4 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 120.20 108.55 11.65 1.50e+00 4.44e-01 6.04e+01 angle pdb=" O3' U 11240 " pdb=" C3' U 11240 " pdb=" C2' U 11240 " ideal model delta sigma weight residual 109.50 119.53 -10.03 1.50e+00 4.44e-01 4.47e+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=" CA GLY I 69 " pdb=" C GLY I 69 " pdb=" O GLY I 69 " ideal model delta sigma weight residual 122.29 117.69 4.60 8.10e-01 1.52e+00 3.22e+01 angle pdb=" N GLU N 39 " pdb=" CA GLU N 39 " pdb=" C GLU N 39 " ideal model delta sigma weight residual 112.13 104.57 7.56 1.37e+00 5.33e-01 3.05e+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: 3245 0.119 - 0.237: 348 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: 3.680 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.570 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 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= 0.554 Angle : 1.024 11.653 28949 Z= 0.689 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 covalent geometry : bond 0.00822 (19801) covalent geometry : angle 1.02408 (28949) hydrogen bonds : bond 0.18020 ( 798) hydrogen bonds : angle 7.52815 ( 1823) metal coordination : bond 0.15162 ( 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 : 0.329 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: C 129 MET cc_start: 0.9303 (mmm) cc_final: 0.8895 (tpp) REVERT: C 153 VAL cc_start: 0.9634 (m) cc_final: 0.9370 (m) REVERT: C 170 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8323 (tm-30) REVERT: C 183 ASP cc_start: 0.8491 (t0) cc_final: 0.8257 (t0) REVERT: G 31 MET cc_start: 0.8782 (ttp) cc_final: 0.8415 (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: 0.7304 (p90) 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: 0.8885 (m-30) REVERT: J 50 THR cc_start: 0.9396 (m) cc_final: 0.8327 (p) REVERT: J 63 ASP cc_start: 0.9308 (t0) cc_final: 0.8830 (t0) REVERT: M 23 TYR cc_start: 0.8794 (t80) cc_final: 0.8325 (t80) REVERT: M 75 MET cc_start: 0.9398 (mmp) cc_final: 0.9180 (mmm) REVERT: M 78 LYS cc_start: 0.9383 (tptp) cc_final: 0.8379 (tptp) REVERT: N 89 MET cc_start: 0.9440 (mmp) cc_final: 0.9159 (mmm) REVERT: S 66 MET cc_start: 0.9245 (mtp) cc_final: 0.8709 (mtp) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1707 time to fit residues: 68.3802 Evaluate side-chains 142 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS B 227 GLN C 32 ASN G 52 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN I 110 GLN J 4 GLN J 56 HIS M 105 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.028247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.022417 restraints weight = 221499.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.023144 restraints weight = 97802.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.023589 restraints weight = 59095.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.023896 restraints weight = 43977.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.024053 restraints weight = 36599.130| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19802 Z= 0.183 Angle : 0.663 7.155 28949 Z= 0.347 Chirality : 0.039 0.290 3609 Planarity : 0.005 0.058 1995 Dihedral : 24.096 174.329 8374 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.04 % Allowed : 17.37 % Favored : 79.59 % 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: -0.80 (0.24), residues: 1092 helix: -0.03 (0.22), residues: 501 sheet: -0.75 (0.39), residues: 164 loop : -0.87 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 139 TYR 0.026 0.002 TYR C 42 PHE 0.026 0.002 PHE B 126 TRP 0.012 0.001 TRP C 201 HIS 0.004 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00361 (19801) covalent geometry : angle 0.66307 (28949) hydrogen bonds : bond 0.06943 ( 798) hydrogen bonds : angle 4.89692 ( 1823) metal coordination : bond 0.00035 ( 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 200 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.381 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: B 42 ASN cc_start: 0.6530 (t0) cc_final: 0.6320 (p0) REVERT: B 122 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8439 (tm-30) REVERT: C 100 GLN cc_start: 0.7886 (tm-30) cc_final: 0.5687 (tm-30) REVERT: C 129 MET cc_start: 0.9234 (mmm) cc_final: 0.8786 (tpp) REVERT: C 142 MET cc_start: 0.9365 (mmm) cc_final: 0.8549 (mmm) REVERT: C 170 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8649 (tm-30) REVERT: C 183 ASP cc_start: 0.8605 (t0) cc_final: 0.8404 (t0) REVERT: C 211 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8315 (mmm) REVERT: G 31 MET cc_start: 0.8871 (ttp) cc_final: 0.8341 (ttp) REVERT: G 38 THR cc_start: 0.9293 (t) cc_final: 0.9004 (t) REVERT: G 140 ASP cc_start: 0.9426 (m-30) cc_final: 0.9210 (m-30) REVERT: I 42 GLU cc_start: 0.8979 (pm20) cc_final: 0.8683 (pp20) REVERT: I 46 MET cc_start: 0.9355 (mmm) cc_final: 0.8885 (mmm) REVERT: J 19 ASP cc_start: 0.9227 (m-30) cc_final: 0.9005 (m-30) REVERT: J 46 LYS cc_start: 0.9365 (mptt) cc_final: 0.9141 (mptt) REVERT: J 63 ASP cc_start: 0.9267 (t0) cc_final: 0.8859 (t0) REVERT: J 66 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8357 (tm-30) REVERT: M 23 TYR cc_start: 0.8759 (t80) cc_final: 0.8197 (t80) REVERT: M 78 LYS cc_start: 0.9336 (tptp) cc_final: 0.8977 (tppt) REVERT: M 81 MET cc_start: 0.8689 (ppp) cc_final: 0.7832 (ppp) REVERT: N 89 MET cc_start: 0.9394 (mmp) cc_final: 0.8941 (mmt) REVERT: S 41 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8675 (m-80) REVERT: S 66 MET cc_start: 0.9307 (mtp) cc_final: 0.8783 (mtp) outliers start: 28 outliers final: 14 residues processed: 187 average time/residue: 0.1372 time to fit residues: 39.6652 Evaluate side-chains 153 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ILE 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 154 SER Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain I residue 54 LEU 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 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 105 ASN 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: 5.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 48 optimal weight: 50.0000 chunk 33 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS B 177 ASN G 52 GLN I 32 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.025900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.020239 restraints weight = 240583.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.020928 restraints weight = 107268.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.021333 restraints weight = 65519.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.021599 restraints weight = 49577.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.021779 restraints weight = 41618.145| |-----------------------------------------------------------------------------| r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 19802 Z= 0.350 Angle : 0.746 7.201 28949 Z= 0.384 Chirality : 0.041 0.302 3609 Planarity : 0.006 0.055 1995 Dihedral : 24.131 177.967 8374 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 27.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.34 % Allowed : 20.20 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.24), residues: 1092 helix: 0.18 (0.22), residues: 507 sheet: -1.02 (0.38), residues: 166 loop : -1.03 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 32 TYR 0.022 0.003 TYR C 42 PHE 0.040 0.003 PHE B 16 TRP 0.040 0.003 TRP G 103 HIS 0.010 0.002 HIS M 12 Details of bonding type rmsd covalent geometry : bond 0.00666 (19801) covalent geometry : angle 0.74561 (28949) hydrogen bonds : bond 0.09311 ( 798) hydrogen bonds : angle 4.93463 ( 1823) metal coordination : bond 0.00030 ( 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 180 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.448 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: B 168 HIS cc_start: 0.9451 (t-90) cc_final: 0.9220 (t-170) REVERT: C 25 ASN cc_start: 0.9380 (m-40) cc_final: 0.9107 (m-40) REVERT: C 129 MET cc_start: 0.9244 (mmm) cc_final: 0.8747 (tpp) REVERT: C 142 MET cc_start: 0.9335 (mmm) cc_final: 0.8739 (mmm) REVERT: C 170 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8616 (tm-30) REVERT: C 183 ASP cc_start: 0.8532 (t0) cc_final: 0.8250 (t0) REVERT: G 29 ILE cc_start: 0.9572 (mm) cc_final: 0.9226 (tt) REVERT: G 31 MET cc_start: 0.8952 (ttp) cc_final: 0.8302 (ttp) REVERT: G 103 TRP cc_start: 0.9680 (m-10) cc_final: 0.9401 (m100) REVERT: I 42 GLU cc_start: 0.9206 (pm20) cc_final: 0.8768 (pp20) REVERT: I 46 MET cc_start: 0.9363 (mmm) cc_final: 0.8923 (mmm) REVERT: I 118 LEU cc_start: 0.9546 (mt) cc_final: 0.9323 (mt) REVERT: I 127 PHE cc_start: 0.8837 (t80) cc_final: 0.8548 (t80) REVERT: J 63 ASP cc_start: 0.9163 (t0) cc_final: 0.8715 (t0) REVERT: J 66 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8388 (tm-30) REVERT: J 88 MET cc_start: 0.9694 (mmm) cc_final: 0.9489 (mmm) REVERT: M 23 TYR cc_start: 0.8574 (t80) cc_final: 0.8168 (t80) REVERT: M 27 LYS cc_start: 0.9480 (tptt) cc_final: 0.9241 (tppt) REVERT: M 62 LYS cc_start: 0.9566 (mtpt) cc_final: 0.9321 (mtmt) REVERT: N 74 LEU cc_start: 0.9541 (mm) cc_final: 0.9319 (mm) REVERT: N 82 ILE cc_start: 0.9414 (mt) cc_final: 0.9077 (mp) REVERT: N 86 GLU cc_start: 0.9421 (mt-10) cc_final: 0.9138 (mp0) REVERT: N 89 MET cc_start: 0.9435 (mmp) cc_final: 0.9057 (mmt) REVERT: S 66 MET cc_start: 0.9312 (mtp) cc_final: 0.8839 (mtp) outliers start: 40 outliers final: 27 residues processed: 165 average time/residue: 0.1305 time to fit residues: 33.5380 Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 PHE 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 B residue 199 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 154 SER 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 I residue 54 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 24 GLU 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 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 136 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** G 86 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.026243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.020472 restraints weight = 236082.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.021164 restraints weight = 105536.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.021568 restraints weight = 64407.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.021870 restraints weight = 48384.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.022000 restraints weight = 40778.987| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19802 Z= 0.247 Angle : 0.656 7.871 28949 Z= 0.341 Chirality : 0.038 0.286 3609 Planarity : 0.005 0.043 1995 Dihedral : 23.993 179.913 8374 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.91 % Allowed : 21.50 % Favored : 74.59 % 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: -0.37 (0.25), residues: 1092 helix: 0.52 (0.22), residues: 507 sheet: -0.94 (0.38), residues: 167 loop : -0.75 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 111 TYR 0.023 0.002 TYR C 168 PHE 0.014 0.002 PHE B 90 TRP 0.015 0.002 TRP G 103 HIS 0.005 0.001 HIS M 14 Details of bonding type rmsd covalent geometry : bond 0.00474 (19801) covalent geometry : angle 0.65607 (28949) hydrogen bonds : bond 0.07586 ( 798) hydrogen bonds : angle 4.66374 ( 1823) metal coordination : bond 0.00037 ( 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 177 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.433 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: C 25 ASN cc_start: 0.9382 (m-40) cc_final: 0.9123 (m-40) REVERT: C 129 MET cc_start: 0.9252 (mmm) cc_final: 0.8788 (tpp) REVERT: C 183 ASP cc_start: 0.8547 (t0) cc_final: 0.8171 (t0) REVERT: G 29 ILE cc_start: 0.9603 (mm) cc_final: 0.9268 (tt) REVERT: G 31 MET cc_start: 0.9022 (ttp) cc_final: 0.8367 (ttp) REVERT: G 103 TRP cc_start: 0.9643 (m-10) cc_final: 0.9396 (m100) REVERT: I 46 MET cc_start: 0.9371 (mmm) cc_final: 0.9169 (mmm) REVERT: J 63 ASP cc_start: 0.9188 (t0) cc_final: 0.8740 (t0) REVERT: J 66 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8256 (tm-30) REVERT: J 88 MET cc_start: 0.9727 (mmm) cc_final: 0.9487 (mmm) REVERT: M 27 LYS cc_start: 0.9448 (tptt) cc_final: 0.8879 (tppt) REVERT: M 31 LYS cc_start: 0.9460 (pttp) cc_final: 0.9128 (pttp) REVERT: N 38 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8742 (p0) REVERT: N 74 LEU cc_start: 0.9530 (mm) cc_final: 0.9310 (mm) REVERT: N 82 ILE cc_start: 0.9386 (mt) cc_final: 0.9059 (mp) REVERT: N 86 GLU cc_start: 0.9376 (mt-10) cc_final: 0.9109 (mp0) REVERT: N 89 MET cc_start: 0.9422 (mmp) cc_final: 0.9076 (mmt) REVERT: S 66 MET cc_start: 0.9361 (mtp) cc_final: 0.8856 (mtp) outliers start: 36 outliers final: 28 residues processed: 164 average time/residue: 0.1264 time to fit residues: 32.6113 Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 PHE 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 62 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 154 SER 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 G residue 133 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 105 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 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 0.4980 chunk 20 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 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 = 0.2745 r_free = 0.2745 target = 0.026356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.020608 restraints weight = 236544.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.021300 restraints weight = 103819.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.021715 restraints weight = 63375.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.022012 restraints weight = 47967.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.022156 restraints weight = 40062.012| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19802 Z= 0.236 Angle : 0.640 8.812 28949 Z= 0.333 Chirality : 0.037 0.282 3609 Planarity : 0.005 0.041 1995 Dihedral : 23.896 178.648 8374 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.56 % Allowed : 21.28 % Favored : 74.16 % 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: 0.63 (0.22), residues: 507 sheet: -0.86 (0.39), residues: 166 loop : -0.71 (0.31), 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 0.014 0.002 PHE G 62 TRP 0.011 0.001 TRP C 201 HIS 0.005 0.001 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00451 (19801) covalent geometry : angle 0.63957 (28949) hydrogen bonds : bond 0.07054 ( 798) hydrogen bonds : angle 4.56329 ( 1823) metal coordination : bond 0.00009 ( 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 173 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 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: B 27 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6432 (mtp) REVERT: B 178 ASN cc_start: 0.9282 (m110) cc_final: 0.9037 (m110) REVERT: C 25 ASN cc_start: 0.9363 (m-40) cc_final: 0.9101 (m-40) REVERT: C 129 MET cc_start: 0.9266 (mmm) cc_final: 0.8723 (tpp) REVERT: C 134 MET cc_start: 0.9601 (ptp) cc_final: 0.9107 (ppp) REVERT: C 183 ASP cc_start: 0.8546 (t0) cc_final: 0.8186 (t0) REVERT: G 29 ILE cc_start: 0.9627 (mm) cc_final: 0.9262 (tt) REVERT: G 31 MET cc_start: 0.9071 (ttp) cc_final: 0.8438 (ttp) REVERT: I 46 MET cc_start: 0.9348 (mmm) cc_final: 0.9139 (mmm) REVERT: I 98 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9187 (mm) REVERT: I 118 LEU cc_start: 0.9555 (mt) cc_final: 0.9304 (mt) REVERT: I 127 PHE cc_start: 0.8879 (t80) cc_final: 0.8660 (t80) REVERT: J 46 LYS cc_start: 0.9386 (mptt) cc_final: 0.8822 (tmmt) REVERT: J 63 ASP cc_start: 0.9193 (t0) cc_final: 0.8761 (t0) REVERT: J 66 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8082 (tm-30) REVERT: J 88 MET cc_start: 0.9751 (mmm) cc_final: 0.9525 (mmm) REVERT: M 27 LYS cc_start: 0.9426 (tptt) cc_final: 0.9105 (tptt) REVERT: M 78 LYS cc_start: 0.9567 (tppt) cc_final: 0.8952 (tppt) REVERT: M 81 MET cc_start: 0.8837 (tmm) cc_final: 0.8490 (ppp) REVERT: N 38 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8719 (p0) REVERT: N 62 ASN cc_start: 0.8930 (m110) cc_final: 0.8365 (p0) REVERT: N 82 ILE cc_start: 0.9394 (mt) cc_final: 0.9071 (mp) REVERT: N 86 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9169 (mp0) REVERT: N 89 MET cc_start: 0.9433 (mmp) cc_final: 0.9020 (mmt) REVERT: S 66 MET cc_start: 0.9382 (mtp) cc_final: 0.8993 (mtp) outliers start: 42 outliers final: 28 residues processed: 158 average time/residue: 0.1230 time to fit residues: 30.5487 Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 30 PHE 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 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 92 GLU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 105 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 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 95 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN B 122 GLN C 102 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN G 52 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.025495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.019952 restraints weight = 239820.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.020604 restraints weight = 106612.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.021004 restraints weight = 66184.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.021285 restraints weight = 50329.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.021423 restraints weight = 42154.375| |-----------------------------------------------------------------------------| r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 19802 Z= 0.344 Angle : 0.724 9.879 28949 Z= 0.373 Chirality : 0.040 0.292 3609 Planarity : 0.006 0.054 1995 Dihedral : 24.029 179.589 8374 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 27.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.86 % Allowed : 22.48 % Favored : 71.66 % 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: -0.39 (0.25), residues: 1092 helix: 0.56 (0.23), residues: 504 sheet: -1.02 (0.39), residues: 164 loop : -0.80 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 131 TYR 0.024 0.003 TYR C 168 PHE 0.016 0.002 PHE B 90 TRP 0.048 0.003 TRP G 103 HIS 0.006 0.002 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00650 (19801) covalent geometry : angle 0.72396 (28949) hydrogen bonds : bond 0.08918 ( 798) hydrogen bonds : angle 4.79160 ( 1823) metal coordination : bond 0.00156 ( 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 180 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 126 time to evaluate : 0.277 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: B 27 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6759 (mtp) REVERT: B 49 MET cc_start: 0.9014 (mmp) cc_final: 0.8780 (mmp) REVERT: B 146 ASN cc_start: 0.9652 (OUTLIER) cc_final: 0.9370 (p0) REVERT: C 25 ASN cc_start: 0.9345 (m-40) cc_final: 0.9105 (m-40) REVERT: C 134 MET cc_start: 0.9589 (ptp) cc_final: 0.9302 (ppp) REVERT: C 183 ASP cc_start: 0.8586 (t0) cc_final: 0.8258 (t0) REVERT: G 29 ILE cc_start: 0.9602 (mm) cc_final: 0.9222 (tt) REVERT: G 31 MET cc_start: 0.9037 (ttp) cc_final: 0.8403 (ttp) REVERT: G 103 TRP cc_start: 0.9675 (m-10) cc_final: 0.9311 (m100) REVERT: I 46 MET cc_start: 0.9309 (mmm) cc_final: 0.9109 (mmm) REVERT: I 98 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9282 (mm) REVERT: I 118 LEU cc_start: 0.9515 (mt) cc_final: 0.9291 (mt) REVERT: I 127 PHE cc_start: 0.8972 (t80) cc_final: 0.8731 (t80) REVERT: J 46 LYS cc_start: 0.9537 (mptt) cc_final: 0.9245 (mppt) REVERT: J 63 ASP cc_start: 0.9167 (t0) cc_final: 0.8766 (t70) REVERT: J 66 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8094 (tm-30) REVERT: J 88 MET cc_start: 0.9774 (mmm) cc_final: 0.9546 (mmm) REVERT: M 27 LYS cc_start: 0.9462 (tptt) cc_final: 0.9156 (tptt) REVERT: M 31 LYS cc_start: 0.9439 (pttp) cc_final: 0.8949 (pttp) REVERT: M 34 LEU cc_start: 0.9455 (tp) cc_final: 0.9085 (tt) REVERT: M 78 LYS cc_start: 0.9595 (tppt) cc_final: 0.9393 (tppt) REVERT: M 81 MET cc_start: 0.8725 (tmm) cc_final: 0.8186 (tmm) REVERT: N 38 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8779 (p0) REVERT: N 82 ILE cc_start: 0.9393 (mt) cc_final: 0.9081 (mp) REVERT: N 89 MET cc_start: 0.9469 (mmp) cc_final: 0.9065 (mmt) REVERT: S 66 MET cc_start: 0.9407 (mtp) cc_final: 0.9004 (mtp) outliers start: 54 outliers final: 34 residues processed: 164 average time/residue: 0.1235 time to fit residues: 31.9897 Evaluate side-chains 153 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 153 ASP 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 154 SER 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 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 92 GLU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 105 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 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 45 optimal weight: 0.5980 chunk 148 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 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** ** S 57 HIS ** 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 = 0.2757 r_free = 0.2757 target = 0.026842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.021123 restraints weight = 232477.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.021832 restraints weight = 100081.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.022233 restraints weight = 60689.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.022531 restraints weight = 45503.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.022692 restraints weight = 38164.325| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19802 Z= 0.153 Angle : 0.613 7.997 28949 Z= 0.319 Chirality : 0.036 0.263 3609 Planarity : 0.005 0.048 1995 Dihedral : 23.835 176.298 8374 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.80 % Allowed : 24.32 % Favored : 71.88 % 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: -0.06 (0.26), residues: 1092 helix: 0.86 (0.23), residues: 506 sheet: -0.84 (0.39), residues: 166 loop : -0.67 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 131 TYR 0.021 0.002 TYR C 168 PHE 0.014 0.001 PHE B 90 TRP 0.038 0.002 TRP G 103 HIS 0.007 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00296 (19801) covalent geometry : angle 0.61251 (28949) hydrogen bonds : bond 0.05981 ( 798) hydrogen bonds : angle 4.44147 ( 1823) metal coordination : bond 0.00860 ( 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: 35 poor density : 128 time to evaluate : 0.510 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: 0.7151 (mtp) cc_final: 0.6926 (mtp) REVERT: B 49 MET cc_start: 0.9011 (mmp) cc_final: 0.8786 (mmp) REVERT: B 122 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8559 (pp30) REVERT: B 154 MET cc_start: 0.6745 (tpp) cc_final: 0.6398 (tpp) REVERT: C 25 ASN cc_start: 0.9328 (m-40) cc_final: 0.9073 (m-40) REVERT: C 134 MET cc_start: 0.9554 (ptp) cc_final: 0.9323 (ppp) REVERT: C 183 ASP cc_start: 0.8514 (t0) cc_final: 0.8126 (t0) REVERT: C 211 MET cc_start: 0.8113 (mmm) cc_final: 0.7862 (mmm) REVERT: G 29 ILE cc_start: 0.9663 (mm) cc_final: 0.9303 (tt) REVERT: G 31 MET cc_start: 0.9057 (ttp) cc_final: 0.8426 (ttp) REVERT: G 101 MET cc_start: 0.9497 (mtp) cc_final: 0.8895 (mtp) REVERT: G 103 TRP cc_start: 0.9663 (m-10) cc_final: 0.9334 (m100) REVERT: I 46 MET cc_start: 0.9338 (mmm) cc_final: 0.9111 (mmm) REVERT: I 57 MET cc_start: 0.9241 (tpp) cc_final: 0.8796 (tpp) REVERT: I 98 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9245 (mm) REVERT: I 118 LEU cc_start: 0.9490 (mt) cc_final: 0.9284 (mt) REVERT: I 127 PHE cc_start: 0.8917 (t80) cc_final: 0.8661 (t80) REVERT: J 63 ASP cc_start: 0.9215 (t0) cc_final: 0.8772 (t0) REVERT: J 66 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8425 (tm-30) REVERT: J 88 MET cc_start: 0.9808 (mmm) cc_final: 0.9579 (mmm) REVERT: M 78 LYS cc_start: 0.9584 (tppt) cc_final: 0.9353 (tppt) REVERT: N 62 ASN cc_start: 0.8869 (m110) cc_final: 0.8252 (p0) REVERT: N 82 ILE cc_start: 0.9234 (mt) cc_final: 0.8987 (mp) REVERT: N 89 MET cc_start: 0.9426 (mmp) cc_final: 0.9056 (mmt) REVERT: S 15 LEU cc_start: 0.9745 (tp) cc_final: 0.9368 (mt) REVERT: S 66 MET cc_start: 0.9358 (mtp) cc_final: 0.8945 (mtp) outliers start: 35 outliers final: 23 residues processed: 152 average time/residue: 0.1248 time to fit residues: 30.0941 Evaluate side-chains 144 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 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 G residue 122 ASN Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 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 16 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 139 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 149 optimal weight: 0.0040 chunk 89 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 190 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 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 = 0.2797 r_free = 0.2797 target = 0.027987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.022379 restraints weight = 226886.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.023122 restraints weight = 96939.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.023557 restraints weight = 58393.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.023862 restraints weight = 43616.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.024004 restraints weight = 36301.575| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19802 Z= 0.127 Angle : 0.598 7.958 28949 Z= 0.312 Chirality : 0.035 0.247 3609 Planarity : 0.004 0.053 1995 Dihedral : 23.594 175.683 8374 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.93 % Allowed : 26.60 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1092 helix: 0.90 (0.23), residues: 507 sheet: -0.54 (0.40), residues: 166 loop : -0.62 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 131 TYR 0.020 0.002 TYR C 168 PHE 0.014 0.001 PHE B 90 TRP 0.031 0.002 TRP G 103 HIS 0.004 0.001 HIS J 70 Details of bonding type rmsd covalent geometry : bond 0.00251 (19801) covalent geometry : angle 0.59825 (28949) hydrogen bonds : bond 0.05110 ( 798) hydrogen bonds : angle 4.32079 ( 1823) metal coordination : bond 0.00054 ( 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 169 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.464 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 27 MET cc_start: 0.7315 (mtp) cc_final: 0.7060 (mtp) REVERT: B 49 MET cc_start: 0.9096 (mmp) cc_final: 0.8812 (mmt) REVERT: B 122 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8303 (pp30) REVERT: B 190 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7757 (m-40) REVERT: C 25 ASN cc_start: 0.9271 (m-40) cc_final: 0.8982 (m-40) REVERT: C 112 ASP cc_start: 0.9094 (t0) cc_final: 0.8306 (m-30) REVERT: C 134 MET cc_start: 0.9531 (ptp) cc_final: 0.9287 (ppp) REVERT: C 142 MET cc_start: 0.9523 (mmm) cc_final: 0.9300 (mmp) REVERT: C 183 ASP cc_start: 0.8586 (t0) cc_final: 0.8373 (t0) REVERT: C 211 MET cc_start: 0.8101 (mmm) cc_final: 0.7890 (mmm) REVERT: G 29 ILE cc_start: 0.9646 (mm) cc_final: 0.9253 (tt) REVERT: G 31 MET cc_start: 0.9008 (ttp) cc_final: 0.8333 (ttp) REVERT: G 52 GLN cc_start: 0.9386 (mm110) cc_final: 0.9089 (pm20) REVERT: G 103 TRP cc_start: 0.9677 (m-10) cc_final: 0.9355 (m100) REVERT: I 46 MET cc_start: 0.9298 (mmm) cc_final: 0.9074 (mmp) REVERT: I 57 MET cc_start: 0.9082 (tpp) cc_final: 0.8724 (tpp) REVERT: I 98 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9211 (mm) REVERT: I 127 PHE cc_start: 0.8849 (t80) cc_final: 0.8551 (t80) REVERT: J 63 ASP cc_start: 0.9247 (t0) cc_final: 0.8798 (t0) REVERT: J 64 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8664 (mm-40) REVERT: J 66 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8344 (tm-30) REVERT: J 88 MET cc_start: 0.9799 (mmm) cc_final: 0.9576 (mmm) REVERT: M 78 LYS cc_start: 0.9583 (tppt) cc_final: 0.9352 (tppt) REVERT: N 62 ASN cc_start: 0.8887 (m110) cc_final: 0.8192 (p0) REVERT: N 89 MET cc_start: 0.9435 (mmp) cc_final: 0.8960 (mmt) REVERT: S 5 LEU cc_start: 0.9524 (mt) cc_final: 0.9264 (mt) REVERT: S 15 LEU cc_start: 0.9732 (tp) cc_final: 0.9398 (mt) REVERT: S 66 MET cc_start: 0.9321 (mtp) cc_final: 0.8921 (mtp) outliers start: 27 outliers final: 18 residues processed: 157 average time/residue: 0.1399 time to fit residues: 33.8840 Evaluate side-chains 153 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 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 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 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 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 S residue 51 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 75 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 52 optimal weight: 0.0970 chunk 46 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.028208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.022625 restraints weight = 225485.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.023380 restraints weight = 95998.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.023807 restraints weight = 58247.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.024102 restraints weight = 43399.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.024239 restraints weight = 36040.352| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19802 Z= 0.127 Angle : 0.612 15.956 28949 Z= 0.317 Chirality : 0.034 0.232 3609 Planarity : 0.004 0.052 1995 Dihedral : 23.524 176.492 8374 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.17 % Allowed : 28.34 % Favored : 69.49 % 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: 0.07 (0.26), residues: 1092 helix: 0.85 (0.23), residues: 512 sheet: -0.38 (0.40), residues: 168 loop : -0.65 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 111 TYR 0.021 0.001 TYR C 168 PHE 0.010 0.001 PHE B 90 TRP 0.030 0.002 TRP G 103 HIS 0.004 0.001 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00252 (19801) covalent geometry : angle 0.61192 (28949) hydrogen bonds : bond 0.05070 ( 798) hydrogen bonds : angle 4.28972 ( 1823) metal coordination : bond 0.00053 ( 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 150 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.375 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: 0.7536 (mtp) cc_final: 0.7160 (mtp) REVERT: B 49 MET cc_start: 0.9166 (mmp) cc_final: 0.8931 (mmt) REVERT: C 25 ASN cc_start: 0.9243 (m-40) cc_final: 0.8916 (m-40) REVERT: C 112 ASP cc_start: 0.9077 (t0) cc_final: 0.8318 (m-30) REVERT: C 129 MET cc_start: 0.8944 (tpp) cc_final: 0.8116 (tpp) REVERT: C 134 MET cc_start: 0.9523 (ptp) cc_final: 0.9280 (ppp) REVERT: C 183 ASP cc_start: 0.8596 (t0) cc_final: 0.8366 (t0) REVERT: G 29 ILE cc_start: 0.9641 (mm) cc_final: 0.9162 (tt) REVERT: G 31 MET cc_start: 0.8986 (ttp) cc_final: 0.8286 (ttp) REVERT: G 103 TRP cc_start: 0.9663 (m-10) cc_final: 0.9332 (m100) REVERT: I 46 MET cc_start: 0.9324 (mmm) cc_final: 0.9090 (mmm) REVERT: I 57 MET cc_start: 0.9082 (tpp) cc_final: 0.8647 (tpp) REVERT: I 61 LEU cc_start: 0.9394 (mt) cc_final: 0.8518 (mt) REVERT: I 98 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9246 (mm) REVERT: I 112 GLU cc_start: 0.8624 (tp30) cc_final: 0.8125 (tp30) REVERT: I 118 LEU cc_start: 0.9426 (mm) cc_final: 0.9039 (tp) REVERT: I 127 PHE cc_start: 0.8832 (t80) cc_final: 0.8488 (t80) REVERT: J 19 ASP cc_start: 0.9310 (m-30) cc_final: 0.9036 (p0) REVERT: J 63 ASP cc_start: 0.9244 (t0) cc_final: 0.8790 (t0) REVERT: J 66 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8285 (tm-30) REVERT: J 88 MET cc_start: 0.9791 (mmm) cc_final: 0.9561 (mmm) REVERT: M 27 LYS cc_start: 0.9264 (tptt) cc_final: 0.8993 (tptp) REVERT: M 103 LYS cc_start: 0.8927 (tptp) cc_final: 0.8400 (tppt) REVERT: N 89 MET cc_start: 0.9412 (mmp) cc_final: 0.9006 (mmt) REVERT: S 5 LEU cc_start: 0.9521 (mt) cc_final: 0.9276 (mt) REVERT: S 66 MET cc_start: 0.9285 (mtp) cc_final: 0.8869 (mtp) outliers start: 20 outliers final: 18 residues processed: 143 average time/residue: 0.1373 time to fit residues: 30.2310 Evaluate side-chains 143 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 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 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 98 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 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 50 THR Chi-restraints excluded: chain S residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 143 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.027395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.021828 restraints weight = 230614.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.022537 restraints weight = 99255.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.022971 restraints weight = 60170.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.023244 restraints weight = 45024.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.023428 restraints weight = 37506.168| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19802 Z= 0.188 Angle : 0.643 13.590 28949 Z= 0.331 Chirality : 0.035 0.237 3609 Planarity : 0.005 0.051 1995 Dihedral : 23.576 179.644 8374 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.50 % Allowed : 28.66 % Favored : 68.84 % 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: 0.07 (0.26), residues: 1092 helix: 0.80 (0.23), residues: 516 sheet: -0.34 (0.41), residues: 168 loop : -0.63 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 53 TYR 0.023 0.002 TYR C 168 PHE 0.010 0.002 PHE I 20 TRP 0.028 0.002 TRP G 103 HIS 0.004 0.001 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00364 (19801) covalent geometry : angle 0.64339 (28949) hydrogen bonds : bond 0.06052 ( 798) hydrogen bonds : angle 4.39300 ( 1823) metal coordination : bond 0.00079 ( 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 150 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.433 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: 0.7620 (mtp) cc_final: 0.7344 (mtp) REVERT: B 49 MET cc_start: 0.9209 (mmp) cc_final: 0.9000 (mmt) REVERT: B 122 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8519 (pp30) REVERT: C 25 ASN cc_start: 0.9253 (m-40) cc_final: 0.8964 (m-40) REVERT: C 129 MET cc_start: 0.8990 (tpp) cc_final: 0.8163 (tpp) REVERT: C 134 MET cc_start: 0.9479 (ptp) cc_final: 0.9245 (ppp) REVERT: C 183 ASP cc_start: 0.8579 (t0) cc_final: 0.8197 (t0) REVERT: G 29 ILE cc_start: 0.9604 (mm) cc_final: 0.9185 (tt) REVERT: G 31 MET cc_start: 0.8953 (ttp) cc_final: 0.8284 (ttp) REVERT: G 52 GLN cc_start: 0.9369 (mm110) cc_final: 0.9136 (pm20) REVERT: G 103 TRP cc_start: 0.9642 (m-10) cc_final: 0.9357 (m100) REVERT: I 46 MET cc_start: 0.9348 (mmm) cc_final: 0.9106 (mmm) REVERT: I 57 MET cc_start: 0.9133 (tpp) cc_final: 0.8635 (tpp) REVERT: I 61 LEU cc_start: 0.9463 (mt) cc_final: 0.8633 (mt) REVERT: I 98 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9286 (mm) REVERT: I 112 GLU cc_start: 0.8810 (tp30) cc_final: 0.8137 (tp30) REVERT: I 127 PHE cc_start: 0.8832 (t80) cc_final: 0.8507 (t80) REVERT: J 19 ASP cc_start: 0.9304 (m-30) cc_final: 0.9085 (p0) REVERT: J 63 ASP cc_start: 0.9192 (t0) cc_final: 0.8699 (t0) REVERT: J 66 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8304 (tm-30) REVERT: J 88 MET cc_start: 0.9805 (mmm) cc_final: 0.9580 (mmm) REVERT: M 27 LYS cc_start: 0.9256 (tptt) cc_final: 0.8901 (tptp) REVERT: M 34 LEU cc_start: 0.9425 (tp) cc_final: 0.9053 (tt) REVERT: N 62 ASN cc_start: 0.8896 (m110) cc_final: 0.8237 (p0) REVERT: N 89 MET cc_start: 0.9518 (mmp) cc_final: 0.8969 (mmt) REVERT: S 5 LEU cc_start: 0.9509 (mt) cc_final: 0.9247 (mt) REVERT: S 66 MET cc_start: 0.9317 (mtp) cc_final: 0.8922 (mtp) outliers start: 23 outliers final: 19 residues processed: 143 average time/residue: 0.1336 time to fit residues: 29.6930 Evaluate side-chains 143 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 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 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 98 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 67 ILE 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 50 THR Chi-restraints excluded: chain S residue 51 VAL 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 42 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** 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 = 0.2727 r_free = 0.2727 target = 0.026043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.020570 restraints weight = 241437.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.021249 restraints weight = 104878.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.021648 restraints weight = 64280.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.021909 restraints weight = 48587.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.022063 restraints weight = 40807.972| |-----------------------------------------------------------------------------| r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19802 Z= 0.297 Angle : 0.731 12.451 28949 Z= 0.375 Chirality : 0.038 0.257 3609 Planarity : 0.006 0.049 1995 Dihedral : 23.803 178.648 8374 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.71 % Allowed : 28.45 % Favored : 68.84 % 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: -0.18 (0.26), residues: 1092 helix: 0.61 (0.23), residues: 513 sheet: -0.56 (0.41), residues: 169 loop : -0.73 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 79 TYR 0.025 0.002 TYR C 168 PHE 0.015 0.002 PHE B 126 TRP 0.024 0.002 TRP G 103 HIS 0.006 0.002 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00566 (19801) covalent geometry : angle 0.73094 (28949) hydrogen bonds : bond 0.08249 ( 798) hydrogen bonds : angle 4.65645 ( 1823) metal coordination : bond 0.00111 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2952.43 seconds wall clock time: 52 minutes 17.14 seconds (3137.14 seconds total)