Starting phenix.real_space_refine on Wed Mar 4 03:27:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b6d_12052/03_2026/7b6d_12052_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b6d_12052/03_2026/7b6d_12052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7b6d_12052/03_2026/7b6d_12052_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b6d_12052/03_2026/7b6d_12052_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b6d_12052/03_2026/7b6d_12052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b6d_12052/03_2026/7b6d_12052.map" } resolution = 4.27 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6713 2.51 5 N 1749 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10470 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "B" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain: "C" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1204 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1741 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 207} Chain: "E" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1177 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "F" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1333 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "G" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1363 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1089 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Time building chain proxies: 2.37, per 1000 atoms: 0.23 Number of scatterers: 10470 At special positions: 0 Unit cell: (167.232, 152.256, 79.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1958 8.00 N 1749 7.00 C 6713 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: 0.94 Conformation dependent library (CDL) restraints added in 552.8 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 43.3% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.567A pdb=" N GLY A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 63 removed outlier: 4.204A pdb=" N LEU A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 84 Processing helix chain 'A' and resid 126 through 140 removed outlier: 4.521A pdb=" N ALA A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'B' and resid 4 through 17 Processing helix chain 'B' and resid 27 through 42 removed outlier: 4.352A pdb=" N GLU B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 107 through 114 removed outlier: 3.814A pdb=" N LYS B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'C' and resid 30 through 53 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'D' and resid 81 through 88 removed outlier: 3.635A pdb=" N ALA D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 165 through 182 removed outlier: 3.810A pdb=" N LEU D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 210 Processing helix chain 'E' and resid 26 through 55 removed outlier: 3.634A pdb=" N ASP E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 Processing helix chain 'E' and resid 122 through 136 Processing helix chain 'F' and resid 32 through 50 Processing helix chain 'F' and resid 52 through 81 removed outlier: 3.573A pdb=" N LEU F 56 " --> pdb=" O THR F 52 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG F 70 " --> pdb=" O ASP F 66 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 removed outlier: 3.898A pdb=" N TRP F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 133 removed outlier: 4.285A pdb=" N PHE F 133 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 160 removed outlier: 3.691A pdb=" N PHE F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 192 Processing helix chain 'G' and resid 14 through 33 Processing helix chain 'G' and resid 35 through 59 removed outlier: 3.703A pdb=" N VAL G 39 " --> pdb=" O ASN G 35 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 55 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU G 56 " --> pdb=" O MET G 52 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP G 57 " --> pdb=" O ARG G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 85 removed outlier: 3.579A pdb=" N PHE G 81 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG G 82 " --> pdb=" O GLN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 removed outlier: 3.539A pdb=" N THR G 121 " --> pdb=" O PRO G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 140 removed outlier: 3.940A pdb=" N SER G 130 " --> pdb=" O SER G 126 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG G 134 " --> pdb=" O SER G 130 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 48 Processing helix chain 'H' and resid 92 through 111 Processing helix chain 'H' and resid 123 through 138 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.223A pdb=" N PHE A 101 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 163 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A 160 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 143 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 80 removed outlier: 4.172A pdb=" N TYR B 86 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 20 removed outlier: 6.129A pdb=" N LEU C 62 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS D 154 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D 5 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 27 through 32 Processing sheet with id=AA5, first strand: chain 'D' and resid 41 through 43 removed outlier: 3.500A pdb=" N ASP D 41 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.616A pdb=" N VAL D 66 " --> pdb=" O MET D 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 15 through 21 removed outlier: 4.233A pdb=" N TYR E 17 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR E 4 " --> pdb=" O PHE E 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 110 through 113 Processing sheet with id=AA9, first strand: chain 'G' and resid 90 through 92 removed outlier: 7.053A pdb=" N GLU G 160 " --> pdb=" O VAL G 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 15 through 20 removed outlier: 3.740A pdb=" N LEU H 15 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA H 2 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP H 84 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS H 4 " --> pdb=" O VAL H 82 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL H 82 " --> pdb=" O CYS H 4 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL H 81 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS H 67 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS H 66 " --> pdb=" O THR H 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR H 61 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLY H 70 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU H 59 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL H 72 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU H 57 " --> pdb=" O VAL H 72 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3391 1.34 - 1.46: 2413 1.46 - 1.58: 4798 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 10683 Sorted by residual: bond pdb=" N GLY H 48 " pdb=" CA GLY H 48 " ideal model delta sigma weight residual 1.449 1.504 -0.055 1.45e-02 4.76e+03 1.44e+01 bond pdb=" C GLY H 48 " pdb=" O GLY H 48 " ideal model delta sigma weight residual 1.235 1.281 -0.046 1.35e-02 5.49e+03 1.16e+01 bond pdb=" C TYR H 30 " pdb=" O TYR H 30 " ideal model delta sigma weight residual 1.235 1.275 -0.039 1.26e-02 6.30e+03 9.74e+00 bond pdb=" N VAL H 39 " pdb=" CA VAL H 39 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.94e+00 bond pdb=" C CYS H 43 " pdb=" O CYS H 43 " ideal model delta sigma weight residual 1.237 1.269 -0.033 1.17e-02 7.31e+03 7.78e+00 ... (remaining 10678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 14038 2.28 - 4.56: 369 4.56 - 6.84: 37 6.84 - 9.11: 5 9.11 - 11.39: 1 Bond angle restraints: 14450 Sorted by residual: angle pdb=" CA LYS H 47 " pdb=" C LYS H 47 " pdb=" O LYS H 47 " ideal model delta sigma weight residual 120.42 115.36 5.06 1.06e+00 8.90e-01 2.28e+01 angle pdb=" C GLU F 109 " pdb=" N LYS F 110 " pdb=" CA LYS F 110 " ideal model delta sigma weight residual 122.37 114.56 7.81 1.72e+00 3.38e-01 2.06e+01 angle pdb=" N LYS H 47 " pdb=" CA LYS H 47 " pdb=" C LYS H 47 " ideal model delta sigma weight residual 111.36 116.29 -4.93 1.09e+00 8.42e-01 2.05e+01 angle pdb=" CA PRO C 138 " pdb=" C PRO C 138 " pdb=" N ILE C 139 " ideal model delta sigma weight residual 115.95 121.01 -5.06 1.12e+00 7.97e-01 2.04e+01 angle pdb=" C PHE G 165 " pdb=" N VAL G 166 " pdb=" CA VAL G 166 " ideal model delta sigma weight residual 123.08 118.78 4.30 1.01e+00 9.80e-01 1.81e+01 ... (remaining 14445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5792 17.84 - 35.68: 553 35.68 - 53.52: 79 53.52 - 71.36: 16 71.36 - 89.20: 11 Dihedral angle restraints: 6451 sinusoidal: 2653 harmonic: 3798 Sorted by residual: dihedral pdb=" CA ASN D 216 " pdb=" C ASN D 216 " pdb=" N ILE D 217 " pdb=" CA ILE D 217 " ideal model delta harmonic sigma weight residual -180.00 -122.18 -57.82 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA PRO D 35 " pdb=" C PRO D 35 " pdb=" N LEU D 36 " pdb=" CA LEU D 36 " ideal model delta harmonic sigma weight residual 180.00 -142.52 -37.48 0 5.00e+00 4.00e-02 5.62e+01 dihedral pdb=" CA ASP C 87 " pdb=" C ASP C 87 " pdb=" N THR C 88 " pdb=" CA THR C 88 " ideal model delta harmonic sigma weight residual -180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 6448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1367 0.068 - 0.137: 231 0.137 - 0.205: 27 0.205 - 0.274: 4 0.274 - 0.342: 2 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CA LYS H 47 " pdb=" N LYS H 47 " pdb=" C LYS H 47 " pdb=" CB LYS H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB ILE F 123 " pdb=" CA ILE F 123 " pdb=" CG1 ILE F 123 " pdb=" CG2 ILE F 123 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE F 72 " pdb=" CA ILE F 72 " pdb=" CG1 ILE F 72 " pdb=" CG2 ILE F 72 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1628 not shown) Planarity restraints: 1849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 48 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLY H 48 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY H 48 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA H 49 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 116 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO A 117 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 117 " 0.051 5.00e-02 4.00e+02 7.80e-02 9.75e+00 pdb=" N PRO A 118 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.043 5.00e-02 4.00e+02 ... (remaining 1846 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 216 2.62 - 3.19: 10941 3.19 - 3.76: 18086 3.76 - 4.33: 25073 4.33 - 4.90: 36828 Nonbonded interactions: 91144 Sorted by model distance: nonbonded pdb=" OH TYR E 102 " pdb=" OD1 ASP F 73 " model vdw 2.049 3.040 nonbonded pdb=" OG SER G 102 " pdb=" NH1 ARG G 162 " model vdw 2.085 3.120 nonbonded pdb=" O GLU A 69 " pdb=" OG1 THR A 73 " model vdw 2.112 3.040 nonbonded pdb=" OD1 ASP A 38 " pdb=" NZ LYS A 41 " model vdw 2.145 3.120 nonbonded pdb=" O TYR F 45 " pdb=" OG SER F 48 " model vdw 2.161 3.040 ... (remaining 91139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'G' and resid 10 through 174) } 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: 6.080 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.005 0.088 10683 Z= 0.249 Angle : 0.875 11.392 14450 Z= 0.521 Chirality : 0.053 0.342 1631 Planarity : 0.006 0.082 1849 Dihedral : 14.401 89.202 3985 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 32.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.20 % Favored : 89.72 % Rotamer: Outliers : 0.43 % Allowed : 0.69 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.22), residues: 1274 helix: -0.82 (0.22), residues: 505 sheet: -1.36 (0.35), residues: 208 loop : -2.48 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 51 TYR 0.021 0.002 TYR F 75 PHE 0.032 0.003 PHE C 82 TRP 0.045 0.003 TRP F 100 HIS 0.008 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00466 (10683) covalent geometry : angle 0.87496 (14450) hydrogen bonds : bond 0.15626 ( 521) hydrogen bonds : angle 7.81290 ( 1482) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8503 (mmp) cc_final: 0.8065 (mmm) REVERT: A 50 MET cc_start: 0.8292 (tmm) cc_final: 0.7942 (tmm) REVERT: A 70 MET cc_start: 0.8530 (tpp) cc_final: 0.8264 (tpp) REVERT: C 56 ASP cc_start: 0.7077 (m-30) cc_final: 0.6637 (t70) REVERT: E 18 GLU cc_start: 0.8481 (pp20) cc_final: 0.8147 (pp20) REVERT: E 42 HIS cc_start: 0.8747 (m-70) cc_final: 0.8439 (t70) REVERT: E 83 ILE cc_start: 0.9205 (mm) cc_final: 0.8792 (tp) REVERT: E 110 MET cc_start: 0.8913 (mpp) cc_final: 0.8580 (mpp) REVERT: E 130 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8450 (tm-30) REVERT: F 124 ILE cc_start: 0.7148 (tt) cc_final: 0.6915 (tp) REVERT: G 148 PHE cc_start: 0.8853 (m-80) cc_final: 0.8511 (m-80) REVERT: H 1 MET cc_start: 0.0673 (mmm) cc_final: 0.0281 (tpt) REVERT: H 16 TYR cc_start: 0.8345 (p90) cc_final: 0.7859 (p90) REVERT: H 102 LEU cc_start: 0.9569 (tp) cc_final: 0.9341 (tt) REVERT: H 122 THR cc_start: 0.6134 (p) cc_final: 0.5795 (t) outliers start: 5 outliers final: 0 residues processed: 135 average time/residue: 0.0889 time to fit residues: 17.6331 Evaluate side-chains 90 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS F 32 GLN ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.040819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.033183 restraints weight = 115665.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.034021 restraints weight = 88449.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.034685 restraints weight = 71577.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.035190 restraints weight = 60243.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.035595 restraints weight = 52218.892| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10683 Z= 0.181 Angle : 0.736 9.244 14450 Z= 0.397 Chirality : 0.047 0.195 1631 Planarity : 0.006 0.054 1849 Dihedral : 7.500 71.854 1405 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.43 % Allowed : 7.12 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.23), residues: 1274 helix: -0.51 (0.22), residues: 518 sheet: -1.48 (0.34), residues: 216 loop : -2.33 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 134 TYR 0.024 0.002 TYR B 17 PHE 0.022 0.002 PHE B 35 TRP 0.023 0.002 TRP F 100 HIS 0.011 0.002 HIS E 51 Details of bonding type rmsd covalent geometry : bond 0.00385 (10683) covalent geometry : angle 0.73625 (14450) hydrogen bonds : bond 0.05235 ( 521) hydrogen bonds : angle 6.38279 ( 1482) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8291 (mmp) cc_final: 0.8049 (mmm) REVERT: A 70 MET cc_start: 0.8510 (tpp) cc_final: 0.8074 (tpp) REVERT: C 41 MET cc_start: 0.8728 (mmm) cc_final: 0.8484 (mtp) REVERT: C 56 ASP cc_start: 0.7444 (m-30) cc_final: 0.6884 (t70) REVERT: E 18 GLU cc_start: 0.8317 (pp20) cc_final: 0.7990 (pp20) REVERT: E 42 HIS cc_start: 0.8641 (m90) cc_final: 0.8386 (m170) REVERT: E 83 ILE cc_start: 0.9305 (mm) cc_final: 0.8987 (tp) REVERT: E 97 PHE cc_start: 0.8222 (t80) cc_final: 0.7944 (t80) REVERT: E 134 ARG cc_start: 0.7345 (mpp-170) cc_final: 0.6835 (mmp80) REVERT: E 138 LEU cc_start: 0.7321 (tp) cc_final: 0.6724 (tp) REVERT: F 147 ASN cc_start: 0.8215 (t0) cc_final: 0.7923 (t0) REVERT: G 43 LEU cc_start: 0.9191 (tt) cc_final: 0.8813 (pp) REVERT: G 148 PHE cc_start: 0.8952 (m-80) cc_final: 0.8484 (m-80) REVERT: H 16 TYR cc_start: 0.8104 (p90) cc_final: 0.7729 (p90) outliers start: 5 outliers final: 2 residues processed: 129 average time/residue: 0.0922 time to fit residues: 17.1145 Evaluate side-chains 85 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 26 optimal weight: 0.0050 chunk 8 optimal weight: 0.0570 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.5112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** 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 = 0.3477 r_free = 0.3477 target = 0.041982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.034220 restraints weight = 113445.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.035115 restraints weight = 86124.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.035791 restraints weight = 69052.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.036327 restraints weight = 57806.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.036738 restraints weight = 49800.644| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10683 Z= 0.152 Angle : 0.691 6.891 14450 Z= 0.369 Chirality : 0.046 0.250 1631 Planarity : 0.005 0.042 1849 Dihedral : 7.027 75.493 1405 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 0.26 % Allowed : 4.72 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.87 (0.23), residues: 1274 helix: -0.15 (0.22), residues: 518 sheet: -1.33 (0.35), residues: 208 loop : -2.25 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 81 TYR 0.037 0.002 TYR E 102 PHE 0.028 0.002 PHE B 35 TRP 0.018 0.001 TRP A 147 HIS 0.007 0.001 HIS E 51 Details of bonding type rmsd covalent geometry : bond 0.00308 (10683) covalent geometry : angle 0.69056 (14450) hydrogen bonds : bond 0.04809 ( 521) hydrogen bonds : angle 5.87602 ( 1482) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8517 (tpp) cc_final: 0.8066 (tpp) REVERT: B 115 PHE cc_start: 0.7725 (t80) cc_final: 0.7316 (t80) REVERT: C 41 MET cc_start: 0.8664 (mmm) cc_final: 0.8381 (mtp) REVERT: C 56 ASP cc_start: 0.7336 (m-30) cc_final: 0.6735 (t70) REVERT: D 69 MET cc_start: 0.7817 (pmm) cc_final: 0.7471 (pmm) REVERT: D 97 LYS cc_start: 0.8356 (mmmt) cc_final: 0.8138 (mmmm) REVERT: E 18 GLU cc_start: 0.8315 (pp20) cc_final: 0.8095 (pp20) REVERT: E 42 HIS cc_start: 0.8640 (m90) cc_final: 0.8282 (m-70) REVERT: E 75 ILE cc_start: 0.8814 (tp) cc_final: 0.8524 (pt) REVERT: E 81 ARG cc_start: 0.8008 (mpt-90) cc_final: 0.6629 (mtt-85) REVERT: E 83 ILE cc_start: 0.9240 (mm) cc_final: 0.8928 (tp) REVERT: E 130 GLU cc_start: 0.8939 (tp30) cc_final: 0.8580 (mt-10) REVERT: F 147 ASN cc_start: 0.8106 (t0) cc_final: 0.7874 (t0) REVERT: F 177 MET cc_start: 0.8046 (tmm) cc_final: 0.7586 (tmm) REVERT: G 105 PHE cc_start: 0.7813 (m-80) cc_final: 0.7371 (m-80) REVERT: G 139 MET cc_start: 0.6976 (tpt) cc_final: 0.6745 (tpp) REVERT: G 148 PHE cc_start: 0.8852 (m-80) cc_final: 0.8350 (m-10) REVERT: H 16 TYR cc_start: 0.8185 (p90) cc_final: 0.7754 (p90) outliers start: 3 outliers final: 0 residues processed: 132 average time/residue: 0.0941 time to fit residues: 18.0890 Evaluate side-chains 88 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.039728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.032211 restraints weight = 118976.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.033092 restraints weight = 89283.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.033736 restraints weight = 70981.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.034269 restraints weight = 59264.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.034668 restraints weight = 50904.245| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 10683 Z= 0.234 Angle : 0.770 7.413 14450 Z= 0.416 Chirality : 0.048 0.181 1631 Planarity : 0.006 0.073 1849 Dihedral : 7.365 73.292 1405 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 29.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 0.17 % Allowed : 7.29 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.23), residues: 1274 helix: -0.50 (0.21), residues: 520 sheet: -1.42 (0.34), residues: 218 loop : -2.36 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 51 TYR 0.031 0.003 TYR F 45 PHE 0.025 0.003 PHE B 112 TRP 0.016 0.002 TRP F 100 HIS 0.013 0.002 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00499 (10683) covalent geometry : angle 0.76971 (14450) hydrogen bonds : bond 0.05086 ( 521) hydrogen bonds : angle 6.13417 ( 1482) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8690 (mmm) cc_final: 0.8364 (mmm) REVERT: A 70 MET cc_start: 0.8193 (tpp) cc_final: 0.7769 (tpp) REVERT: C 41 MET cc_start: 0.8643 (mmm) cc_final: 0.8438 (mtp) REVERT: E 42 HIS cc_start: 0.8676 (m90) cc_final: 0.8376 (m170) REVERT: E 130 GLU cc_start: 0.8805 (tp30) cc_final: 0.8569 (mt-10) REVERT: F 147 ASN cc_start: 0.7981 (t0) cc_final: 0.7705 (t0) REVERT: G 105 PHE cc_start: 0.7995 (m-80) cc_final: 0.7340 (m-80) REVERT: G 139 MET cc_start: 0.7336 (tpt) cc_final: 0.6828 (tpt) REVERT: G 148 PHE cc_start: 0.8984 (m-80) cc_final: 0.8429 (m-10) REVERT: H 16 TYR cc_start: 0.8234 (p90) cc_final: 0.7860 (p90) REVERT: H 67 LYS cc_start: 0.8077 (mmpt) cc_final: 0.7809 (tmtt) REVERT: H 124 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8306 (tptt) outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.0937 time to fit residues: 15.7094 Evaluate side-chains 81 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 112 optimal weight: 0.0870 chunk 123 optimal weight: 0.0770 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 42 optimal weight: 0.0170 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** 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 = 0.3476 r_free = 0.3476 target = 0.041685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.033854 restraints weight = 113651.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.034755 restraints weight = 86485.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.035435 restraints weight = 69373.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.035988 restraints weight = 58067.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.036412 restraints weight = 50058.175| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10683 Z= 0.144 Angle : 0.697 8.110 14450 Z= 0.372 Chirality : 0.047 0.248 1631 Planarity : 0.005 0.050 1849 Dihedral : 6.814 74.463 1405 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.23), residues: 1274 helix: -0.16 (0.22), residues: 518 sheet: -1.30 (0.34), residues: 207 loop : -2.19 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 81 TYR 0.029 0.002 TYR E 102 PHE 0.020 0.002 PHE H 99 TRP 0.011 0.001 TRP A 147 HIS 0.008 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00305 (10683) covalent geometry : angle 0.69703 (14450) hydrogen bonds : bond 0.04596 ( 521) hydrogen bonds : angle 5.67807 ( 1482) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8855 (mmm) cc_final: 0.8484 (mmm) REVERT: A 70 MET cc_start: 0.8335 (tpp) cc_final: 0.7863 (tpp) REVERT: C 1 MET cc_start: 0.6846 (mmm) cc_final: 0.6635 (mmp) REVERT: C 41 MET cc_start: 0.8652 (mmm) cc_final: 0.8394 (mtp) REVERT: E 18 GLU cc_start: 0.8296 (pp20) cc_final: 0.8093 (pp20) REVERT: E 42 HIS cc_start: 0.8665 (m90) cc_final: 0.8440 (m-70) REVERT: E 81 ARG cc_start: 0.7463 (mpt90) cc_final: 0.6863 (mmt-90) REVERT: E 83 ILE cc_start: 0.9289 (mm) cc_final: 0.9008 (tp) REVERT: E 130 GLU cc_start: 0.8816 (tp30) cc_final: 0.8569 (mt-10) REVERT: E 138 LEU cc_start: 0.7477 (tp) cc_final: 0.7224 (mt) REVERT: F 113 HIS cc_start: 0.8620 (p-80) cc_final: 0.8314 (p-80) REVERT: F 147 ASN cc_start: 0.8218 (t0) cc_final: 0.7943 (t0) REVERT: F 177 MET cc_start: 0.8238 (tmm) cc_final: 0.8034 (tmm) REVERT: G 29 MET cc_start: 0.8820 (mmp) cc_final: 0.8613 (mmp) REVERT: G 105 PHE cc_start: 0.7918 (m-80) cc_final: 0.7395 (m-80) REVERT: G 148 PHE cc_start: 0.8870 (m-80) cc_final: 0.8359 (m-80) REVERT: H 16 TYR cc_start: 0.8189 (p90) cc_final: 0.7782 (p90) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0979 time to fit residues: 17.6914 Evaluate side-chains 88 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.041253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.033427 restraints weight = 114760.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.034300 restraints weight = 87581.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.034957 restraints weight = 70490.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.035496 restraints weight = 59205.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.035909 restraints weight = 51171.409| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10683 Z= 0.141 Angle : 0.670 7.576 14450 Z= 0.357 Chirality : 0.046 0.213 1631 Planarity : 0.004 0.044 1849 Dihedral : 6.600 73.999 1405 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.65 (0.23), residues: 1274 helix: -0.02 (0.22), residues: 515 sheet: -1.19 (0.34), residues: 207 loop : -2.07 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 134 TYR 0.031 0.002 TYR B 32 PHE 0.012 0.002 PHE F 94 TRP 0.009 0.001 TRP F 100 HIS 0.009 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00304 (10683) covalent geometry : angle 0.66967 (14450) hydrogen bonds : bond 0.04468 ( 521) hydrogen bonds : angle 5.54881 ( 1482) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8808 (mmm) cc_final: 0.8407 (mmm) REVERT: A 70 MET cc_start: 0.8292 (tpp) cc_final: 0.7846 (tpp) REVERT: C 41 MET cc_start: 0.8606 (mmm) cc_final: 0.8355 (mtp) REVERT: E 1 MET cc_start: 0.5470 (ppp) cc_final: 0.5204 (ppp) REVERT: E 18 GLU cc_start: 0.8367 (pp20) cc_final: 0.8165 (pp20) REVERT: E 81 ARG cc_start: 0.7739 (mpt90) cc_final: 0.6923 (mmt180) REVERT: E 83 ILE cc_start: 0.9261 (mm) cc_final: 0.8969 (tp) REVERT: E 130 GLU cc_start: 0.8803 (tp30) cc_final: 0.8541 (mt-10) REVERT: E 134 ARG cc_start: 0.7786 (mpp-170) cc_final: 0.7466 (mmp80) REVERT: E 138 LEU cc_start: 0.7516 (tp) cc_final: 0.7259 (mt) REVERT: F 113 HIS cc_start: 0.8564 (p-80) cc_final: 0.8272 (p-80) REVERT: F 163 PRO cc_start: 0.7923 (Cg_exo) cc_final: 0.7713 (Cg_endo) REVERT: G 105 PHE cc_start: 0.7894 (m-80) cc_final: 0.7298 (m-80) REVERT: G 148 PHE cc_start: 0.8875 (m-80) cc_final: 0.8088 (m-80) REVERT: H 16 TYR cc_start: 0.8127 (p90) cc_final: 0.7726 (p90) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.0900 time to fit residues: 16.2311 Evaluate side-chains 86 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 74 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.041435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.033633 restraints weight = 112936.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.034489 restraints weight = 86659.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.035160 restraints weight = 70128.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.035677 restraints weight = 59046.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.036082 restraints weight = 51339.058| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10683 Z= 0.139 Angle : 0.672 7.184 14450 Z= 0.359 Chirality : 0.046 0.248 1631 Planarity : 0.004 0.041 1849 Dihedral : 6.401 68.141 1405 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.55 (0.23), residues: 1274 helix: 0.07 (0.22), residues: 521 sheet: -1.12 (0.35), residues: 202 loop : -2.06 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 134 TYR 0.020 0.002 TYR G 48 PHE 0.016 0.002 PHE H 99 TRP 0.009 0.001 TRP G 94 HIS 0.008 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00302 (10683) covalent geometry : angle 0.67248 (14450) hydrogen bonds : bond 0.04387 ( 521) hydrogen bonds : angle 5.39682 ( 1482) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8879 (mmm) cc_final: 0.8530 (mmm) REVERT: A 52 MET cc_start: 0.7016 (mmt) cc_final: 0.6796 (mmt) REVERT: A 70 MET cc_start: 0.8220 (tpp) cc_final: 0.7796 (tpp) REVERT: C 41 MET cc_start: 0.8572 (mmm) cc_final: 0.8344 (mtp) REVERT: E 1 MET cc_start: 0.5562 (ppp) cc_final: 0.5302 (ppp) REVERT: E 81 ARG cc_start: 0.7646 (mpt90) cc_final: 0.6748 (mmt180) REVERT: E 83 ILE cc_start: 0.9259 (mm) cc_final: 0.8976 (tp) REVERT: E 130 GLU cc_start: 0.8701 (tp30) cc_final: 0.8455 (mt-10) REVERT: F 113 HIS cc_start: 0.8685 (p-80) cc_final: 0.8367 (p-80) REVERT: F 163 PRO cc_start: 0.7981 (Cg_exo) cc_final: 0.7775 (Cg_endo) REVERT: G 29 MET cc_start: 0.8853 (mmp) cc_final: 0.8638 (mmp) REVERT: G 70 MET cc_start: 0.6830 (mmt) cc_final: 0.6541 (mmm) REVERT: G 105 PHE cc_start: 0.7919 (m-80) cc_final: 0.7493 (m-80) REVERT: G 148 PHE cc_start: 0.8966 (m-80) cc_final: 0.8144 (m-80) REVERT: H 16 TYR cc_start: 0.8190 (p90) cc_final: 0.7780 (p90) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0924 time to fit residues: 15.7932 Evaluate side-chains 87 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 0.4980 chunk 100 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.040365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.032633 restraints weight = 116846.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.033496 restraints weight = 88856.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.034156 restraints weight = 71408.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.034676 restraints weight = 59952.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.035070 restraints weight = 51944.548| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10683 Z= 0.185 Angle : 0.721 7.632 14450 Z= 0.388 Chirality : 0.047 0.223 1631 Planarity : 0.005 0.040 1849 Dihedral : 6.602 69.481 1405 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.23), residues: 1274 helix: -0.20 (0.22), residues: 523 sheet: -1.15 (0.34), residues: 215 loop : -2.08 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 134 TYR 0.031 0.002 TYR B 32 PHE 0.017 0.002 PHE C 140 TRP 0.016 0.002 TRP F 100 HIS 0.008 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00406 (10683) covalent geometry : angle 0.72070 (14450) hydrogen bonds : bond 0.04640 ( 521) hydrogen bonds : angle 5.63566 ( 1482) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8738 (mmm) cc_final: 0.8451 (mmm) REVERT: A 52 MET cc_start: 0.7387 (mmt) cc_final: 0.7168 (mmt) REVERT: A 70 MET cc_start: 0.8077 (tpp) cc_final: 0.7683 (tpp) REVERT: B 115 PHE cc_start: 0.7700 (t80) cc_final: 0.7418 (t80) REVERT: E 18 GLU cc_start: 0.8549 (pp20) cc_final: 0.8159 (pp20) REVERT: E 81 ARG cc_start: 0.7630 (mpt90) cc_final: 0.7318 (mmt180) REVERT: E 134 ARG cc_start: 0.7879 (mpp-170) cc_final: 0.7358 (mmt180) REVERT: E 138 LEU cc_start: 0.6797 (mt) cc_final: 0.6298 (mt) REVERT: F 113 HIS cc_start: 0.8593 (p-80) cc_final: 0.8284 (p-80) REVERT: G 105 PHE cc_start: 0.7886 (m-80) cc_final: 0.7360 (m-80) REVERT: G 148 PHE cc_start: 0.8966 (m-80) cc_final: 0.8239 (m-80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0897 time to fit residues: 15.8337 Evaluate side-chains 86 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS E 35 HIS E 42 HIS ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.040644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.032944 restraints weight = 115448.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.033808 restraints weight = 87883.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.034483 restraints weight = 70620.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.035003 restraints weight = 59144.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.035415 restraints weight = 51129.949| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10683 Z= 0.162 Angle : 0.708 8.381 14450 Z= 0.378 Chirality : 0.047 0.211 1631 Planarity : 0.005 0.052 1849 Dihedral : 6.546 71.686 1405 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.70 (0.23), residues: 1274 helix: -0.12 (0.22), residues: 521 sheet: -1.23 (0.34), residues: 206 loop : -2.05 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 134 TYR 0.026 0.002 TYR G 48 PHE 0.036 0.002 PHE D 186 TRP 0.010 0.001 TRP F 100 HIS 0.007 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00360 (10683) covalent geometry : angle 0.70771 (14450) hydrogen bonds : bond 0.04547 ( 521) hydrogen bonds : angle 5.56064 ( 1482) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8698 (mmm) cc_final: 0.8360 (mmm) REVERT: A 52 MET cc_start: 0.7380 (mmt) cc_final: 0.7133 (mmt) REVERT: A 70 MET cc_start: 0.8071 (tpp) cc_final: 0.7673 (tpp) REVERT: B 115 PHE cc_start: 0.7660 (t80) cc_final: 0.7356 (t80) REVERT: E 18 GLU cc_start: 0.8462 (pp20) cc_final: 0.8071 (pp20) REVERT: E 81 ARG cc_start: 0.7614 (mpt90) cc_final: 0.7335 (mmt180) REVERT: E 134 ARG cc_start: 0.7981 (mpp-170) cc_final: 0.7453 (mmt180) REVERT: E 138 LEU cc_start: 0.6741 (mt) cc_final: 0.6263 (mt) REVERT: F 113 HIS cc_start: 0.8563 (p-80) cc_final: 0.8254 (p-80) REVERT: G 105 PHE cc_start: 0.7846 (m-80) cc_final: 0.7296 (m-80) REVERT: G 148 PHE cc_start: 0.8943 (m-80) cc_final: 0.8203 (m-80) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0944 time to fit residues: 16.3120 Evaluate side-chains 86 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 74 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.041074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.033390 restraints weight = 113922.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.034268 restraints weight = 86590.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.034943 restraints weight = 69361.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.035476 restraints weight = 57976.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.035885 restraints weight = 49941.059| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10683 Z= 0.143 Angle : 0.701 7.747 14450 Z= 0.372 Chirality : 0.046 0.198 1631 Planarity : 0.005 0.064 1849 Dihedral : 6.215 64.759 1405 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.58 (0.23), residues: 1274 helix: -0.02 (0.22), residues: 521 sheet: -1.10 (0.35), residues: 208 loop : -2.01 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 134 TYR 0.035 0.002 TYR B 32 PHE 0.023 0.002 PHE D 186 TRP 0.009 0.001 TRP G 94 HIS 0.006 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00316 (10683) covalent geometry : angle 0.70093 (14450) hydrogen bonds : bond 0.04319 ( 521) hydrogen bonds : angle 5.42797 ( 1482) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8747 (mmm) cc_final: 0.8465 (mmm) REVERT: A 70 MET cc_start: 0.8245 (tpp) cc_final: 0.7819 (tpp) REVERT: B 115 PHE cc_start: 0.7631 (t80) cc_final: 0.7157 (t80) REVERT: C 56 ASP cc_start: 0.7707 (m-30) cc_final: 0.6966 (t70) REVERT: D 69 MET cc_start: 0.7160 (pmm) cc_final: 0.6783 (pmm) REVERT: E 18 GLU cc_start: 0.8319 (pp20) cc_final: 0.7999 (pp20) REVERT: E 81 ARG cc_start: 0.7622 (mpt90) cc_final: 0.7221 (mmt90) REVERT: E 130 GLU cc_start: 0.8714 (tp30) cc_final: 0.8355 (mt-10) REVERT: E 138 LEU cc_start: 0.6798 (mt) cc_final: 0.6385 (mt) REVERT: F 113 HIS cc_start: 0.8549 (p-80) cc_final: 0.8254 (p-80) REVERT: F 182 ASP cc_start: 0.9070 (t0) cc_final: 0.8778 (t0) REVERT: G 105 PHE cc_start: 0.7523 (m-80) cc_final: 0.7277 (m-80) REVERT: G 148 PHE cc_start: 0.8763 (m-80) cc_final: 0.8164 (m-80) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0978 time to fit residues: 16.8192 Evaluate side-chains 93 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 57 optimal weight: 0.0020 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 122 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 10 optimal weight: 0.0470 chunk 24 optimal weight: 3.9990 overall best weight: 0.6248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.041493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.033751 restraints weight = 113259.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.034632 restraints weight = 85934.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.035313 restraints weight = 68911.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.035838 restraints weight = 57563.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.036219 restraints weight = 49693.368| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10683 Z= 0.138 Angle : 0.698 8.364 14450 Z= 0.368 Chirality : 0.046 0.194 1631 Planarity : 0.004 0.045 1849 Dihedral : 6.084 71.365 1405 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.44 (0.24), residues: 1274 helix: 0.10 (0.22), residues: 520 sheet: -1.01 (0.35), residues: 208 loop : -1.95 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 134 TYR 0.026 0.002 TYR B 17 PHE 0.019 0.001 PHE B 35 TRP 0.008 0.001 TRP G 94 HIS 0.005 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00307 (10683) covalent geometry : angle 0.69790 (14450) hydrogen bonds : bond 0.04338 ( 521) hydrogen bonds : angle 5.34914 ( 1482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1609.52 seconds wall clock time: 28 minutes 56.91 seconds (1736.91 seconds total)