Starting phenix.real_space_refine on Mon Jul 28 15:46:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b6x_12057/07_2025/7b6x_12057.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b6x_12057/07_2025/7b6x_12057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b6x_12057/07_2025/7b6x_12057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b6x_12057/07_2025/7b6x_12057.map" model { file = "/net/cci-nas-00/data/ceres_data/7b6x_12057/07_2025/7b6x_12057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b6x_12057/07_2025/7b6x_12057.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.91, per 1000 atoms: 0.66 Number of scatterers: 10470 At special positions: 0 Unit cell: (172.127, 148.255, 74.1276, 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: 2.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 38 helices and 10 sheets defined 43.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 16 through 33 removed outlier: 3.783A pdb=" N LEU A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 62 removed outlier: 4.250A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 85 Processing helix chain 'A' and resid 126 through 140 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'B' and resid 3 through 17 removed outlier: 4.318A pdb=" N PHE B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 42 Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.699A pdb=" N ARG B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 115 removed outlier: 4.126A pdb=" N PHE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'D' and resid 104 through 121 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 166 through 182 Processing helix chain 'D' and resid 195 through 211 Processing helix chain 'E' and resid 26 through 55 removed outlier: 4.588A pdb=" N GLU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 110 removed outlier: 3.890A pdb=" N ASN E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'F' and resid 32 through 50 Processing helix chain 'F' and resid 52 through 78 removed outlier: 4.041A pdb=" N ARG F 70 " --> pdb=" O ASP F 66 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 Processing helix chain 'F' and resid 129 through 133 removed outlier: 3.623A pdb=" N THR F 132 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 161 Processing helix chain 'F' and resid 181 through 191 Processing helix chain 'G' and resid 14 through 33 removed outlier: 3.554A pdb=" N LEU G 18 " --> pdb=" O ASN G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 62 removed outlier: 3.552A pdb=" N MET G 52 " --> pdb=" O TYR G 48 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU G 56 " --> pdb=" O MET G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 85 removed outlier: 3.605A pdb=" N THR G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 removed outlier: 3.705A pdb=" N THR G 121 " --> pdb=" O PRO G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 127 through 140 Processing helix chain 'G' and resid 151 through 155 removed outlier: 3.712A pdb=" N GLY G 155 " --> pdb=" O GLN G 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.884A pdb=" N VAL H 95 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 138 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.731A pdb=" N VAL A 163 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 103 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 161 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU A 160 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 164 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 145 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 166 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU A 143 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.597A 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: 6.908A pdb=" N ILE C 8 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR C 18 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 6 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN C 5 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 64 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR C 63 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU D 135 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 143 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 8 " --> pdb=" O ILE D 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 27 through 32 removed outlier: 4.071A pdb=" N LYS D 30 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 96 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA D 65 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER D 99 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU D 63 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL D 64 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 71 " --> pdb=" O VAL D 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 40 through 43 Processing sheet with id=AA6, first strand: chain 'E' and resid 15 through 20 removed outlier: 3.583A pdb=" N TYR E 5 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 83 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS E 86 " --> pdb=" O PHE E 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 110 through 113 removed outlier: 3.509A pdb=" N ILE F 124 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 100 through 101 removed outlier: 3.505A pdb=" N PHE G 101 " --> pdb=" O VAL G 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 100 through 101 removed outlier: 3.505A pdb=" N PHE G 101 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU G 160 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLU G 143 " --> pdb=" O VAL G 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.677A pdb=" N TYR H 61 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY H 70 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU H 59 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N VAL H 72 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU H 57 " --> pdb=" O VAL H 72 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1425 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: 2.79 Time building geometry restraints manager: 3.26 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: 3376 1.34 - 1.46: 2294 1.46 - 1.58: 4932 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 10683 Sorted by residual: bond pdb=" C GLU F 127 " pdb=" N PRO F 128 " ideal model delta sigma weight residual 1.334 1.292 0.042 1.11e-02 8.12e+03 1.41e+01 bond pdb=" C HIS D 61 " pdb=" N VAL D 62 " ideal model delta sigma weight residual 1.334 1.292 0.041 1.24e-02 6.50e+03 1.11e+01 bond pdb=" C TRP C 115 " pdb=" N THR C 116 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.47e-02 4.63e+03 1.09e+01 bond pdb=" CB PHE A 17 " pdb=" CG PHE A 17 " ideal model delta sigma weight residual 1.502 1.448 0.054 2.30e-02 1.89e+03 5.53e+00 bond pdb=" CB ARG D 100 " pdb=" CG ARG D 100 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.24e+00 ... (remaining 10678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 14099 2.91 - 5.83: 308 5.83 - 8.74: 37 8.74 - 11.66: 5 11.66 - 14.57: 1 Bond angle restraints: 14450 Sorted by residual: angle pdb=" CB LEU D 197 " pdb=" CG LEU D 197 " pdb=" CD1 LEU D 197 " ideal model delta sigma weight residual 110.70 125.27 -14.57 3.00e+00 1.11e-01 2.36e+01 angle pdb=" C PRO A 65 " pdb=" N ARG A 66 " pdb=" CA ARG A 66 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C ASN B 16 " pdb=" N TYR B 17 " pdb=" CA TYR B 17 " ideal model delta sigma weight residual 122.19 116.63 5.56 1.41e+00 5.03e-01 1.56e+01 angle pdb=" CB MET A 70 " pdb=" CG MET A 70 " pdb=" SD MET A 70 " ideal model delta sigma weight residual 112.70 123.46 -10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C VAL A 114 " pdb=" N GLU A 115 " pdb=" CA GLU A 115 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 ... (remaining 14445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5726 17.41 - 34.82: 628 34.82 - 52.23: 75 52.23 - 69.64: 11 69.64 - 87.05: 11 Dihedral angle restraints: 6451 sinusoidal: 2653 harmonic: 3798 Sorted by residual: dihedral pdb=" CA ILE D 214 " pdb=" C ILE D 214 " pdb=" N SER D 215 " pdb=" CA SER D 215 " ideal model delta harmonic sigma weight residual 180.00 140.32 39.68 0 5.00e+00 4.00e-02 6.30e+01 dihedral pdb=" CA ILE F 134 " pdb=" C ILE F 134 " pdb=" N SER F 135 " pdb=" CA SER F 135 " ideal model delta harmonic sigma weight residual -180.00 -141.08 -38.92 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA SER A 15 " pdb=" C SER A 15 " pdb=" N GLU A 16 " pdb=" CA GLU A 16 " ideal model delta harmonic sigma weight residual 180.00 153.27 26.73 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 6448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1414 0.083 - 0.166: 202 0.166 - 0.248: 9 0.248 - 0.331: 3 0.331 - 0.414: 3 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CB ILE F 134 " pdb=" CA ILE F 134 " pdb=" CG1 ILE F 134 " pdb=" CG2 ILE F 134 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CG LEU D 197 " pdb=" CB LEU D 197 " pdb=" CD1 LEU D 197 " pdb=" CD2 LEU D 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB ILE C 142 " pdb=" CA ILE C 142 " pdb=" CG1 ILE C 142 " pdb=" CG2 ILE C 142 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 1628 not shown) Planarity restraints: 1849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 117 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO A 118 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 136 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO F 137 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO F 137 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 137 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 16 " -0.020 2.00e-02 2.50e+03 1.63e-02 5.31e+00 pdb=" CG TYR H 16 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR H 16 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR H 16 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR H 16 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 16 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 16 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 16 " -0.003 2.00e-02 2.50e+03 ... (remaining 1846 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 269 2.61 - 3.18: 11331 3.18 - 3.75: 18377 3.75 - 4.33: 25203 4.33 - 4.90: 37379 Nonbonded interactions: 92559 Sorted by model distance: nonbonded pdb=" O PHE B 61 " pdb=" OG1 THR B 64 " model vdw 2.035 3.040 nonbonded pdb=" OD1 ASN C 67 " pdb=" OG SER D 132 " model vdw 2.056 3.040 nonbonded pdb=" OG SER G 102 " pdb=" NH1 ARG G 162 " model vdw 2.079 3.120 nonbonded pdb=" OG1 THR C 30 " pdb=" OE1 GLU C 33 " model vdw 2.082 3.040 nonbonded pdb=" NH2 ARG B 51 " pdb=" O LEU H 44 " model vdw 2.085 3.120 ... (remaining 92554 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: 5.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.930 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 0.088 10683 Z= 0.359 Angle : 1.062 14.570 14450 Z= 0.575 Chirality : 0.058 0.414 1631 Planarity : 0.006 0.076 1849 Dihedral : 14.167 87.051 3985 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 44.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.34 % Favored : 86.66 % Rotamer: Outliers : 0.09 % Allowed : 0.51 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.22), residues: 1274 helix: -1.11 (0.21), residues: 520 sheet: -1.58 (0.38), residues: 180 loop : -2.59 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 147 HIS 0.017 0.003 HIS F 113 PHE 0.037 0.004 PHE F 133 TYR 0.040 0.004 TYR H 16 ARG 0.038 0.002 ARG H 128 Details of bonding type rmsd hydrogen bonds : bond 0.18238 ( 496) hydrogen bonds : angle 8.07276 ( 1425) covalent geometry : bond 0.00777 (10683) covalent geometry : angle 1.06183 (14450) *********************** 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 141 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8539 (m-30) cc_final: 0.8142 (m-30) REVERT: B 59 MET cc_start: 0.8798 (pmm) cc_final: 0.8507 (pmm) REVERT: D 110 PHE cc_start: 0.8741 (t80) cc_final: 0.8416 (t80) REVERT: D 194 ARG cc_start: 0.7068 (mpp80) cc_final: 0.6651 (mpp80) REVERT: E 105 TYR cc_start: 0.8893 (t80) cc_final: 0.8421 (t80) REVERT: F 55 GLU cc_start: 0.8685 (pt0) cc_final: 0.8434 (tm-30) REVERT: F 177 MET cc_start: 0.7210 (tmm) cc_final: 0.6873 (tmm) REVERT: G 91 ILE cc_start: 0.3688 (mp) cc_final: 0.3208 (mt) REVERT: H 102 LEU cc_start: 0.8638 (tt) cc_final: 0.8157 (tp) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.2075 time to fit residues: 42.9586 Evaluate side-chains 104 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 GLN A 122 ASN A 152 GLN B 25 HIS B 146 HIS ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.064346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.054609 restraints weight = 74329.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.056020 restraints weight = 50339.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.057004 restraints weight = 37502.151| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10683 Z= 0.171 Angle : 0.768 7.789 14450 Z= 0.404 Chirality : 0.048 0.228 1631 Planarity : 0.006 0.076 1849 Dihedral : 7.395 83.038 1408 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 1.03 % Allowed : 11.58 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.23), residues: 1274 helix: -0.45 (0.22), residues: 531 sheet: -1.35 (0.38), residues: 190 loop : -2.43 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 147 HIS 0.010 0.002 HIS F 113 PHE 0.027 0.002 PHE B 35 TYR 0.028 0.002 TYR D 180 ARG 0.015 0.001 ARG F 59 Details of bonding type rmsd hydrogen bonds : bond 0.05366 ( 496) hydrogen bonds : angle 6.08601 ( 1425) covalent geometry : bond 0.00382 (10683) covalent geometry : angle 0.76759 (14450) *********************** 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 153 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8383 (t0) cc_final: 0.7900 (t0) REVERT: A 41 LYS cc_start: 0.8553 (mppt) cc_final: 0.8277 (tptt) REVERT: A 70 MET cc_start: 0.7988 (mmm) cc_final: 0.7786 (mmm) REVERT: A 99 ASP cc_start: 0.8592 (m-30) cc_final: 0.8234 (m-30) REVERT: A 106 ASP cc_start: 0.7703 (t70) cc_final: 0.7345 (m-30) REVERT: A 113 PHE cc_start: 0.4764 (t80) cc_final: 0.4540 (t80) REVERT: D 110 PHE cc_start: 0.8744 (t80) cc_final: 0.8357 (t80) REVERT: E 5 TYR cc_start: 0.6041 (t80) cc_final: 0.5610 (t80) REVERT: E 101 MET cc_start: 0.8109 (mmm) cc_final: 0.7869 (mmm) REVERT: E 105 TYR cc_start: 0.8554 (t80) cc_final: 0.8186 (t80) REVERT: F 39 PHE cc_start: 0.7239 (t80) cc_final: 0.7007 (t80) REVERT: F 55 GLU cc_start: 0.8578 (pt0) cc_final: 0.8115 (tm-30) REVERT: F 169 HIS cc_start: 0.6875 (m-70) cc_final: 0.6672 (m-70) REVERT: G 91 ILE cc_start: 0.3629 (mp) cc_final: 0.3090 (mt) REVERT: H 102 LEU cc_start: 0.8579 (tt) cc_final: 0.8195 (tp) outliers start: 12 outliers final: 7 residues processed: 149 average time/residue: 0.2204 time to fit residues: 47.6052 Evaluate side-chains 118 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 0.0000 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN B 25 HIS ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.064820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.055002 restraints weight = 75213.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.056415 restraints weight = 50579.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.057461 restraints weight = 37586.465| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2427 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 : 0.706 8.330 14450 Z= 0.370 Chirality : 0.045 0.169 1631 Planarity : 0.005 0.072 1849 Dihedral : 6.868 82.999 1408 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.83 % Allowed : 15.95 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.23), residues: 1274 helix: -0.05 (0.22), residues: 523 sheet: -1.24 (0.40), residues: 184 loop : -2.31 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 170 HIS 0.008 0.001 HIS F 113 PHE 0.022 0.002 PHE B 35 TYR 0.024 0.002 TYR C 69 ARG 0.017 0.001 ARG F 59 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 496) hydrogen bonds : angle 5.70813 ( 1425) covalent geometry : bond 0.00334 (10683) covalent geometry : angle 0.70639 (14450) *********************** 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 173 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8348 (t0) cc_final: 0.7862 (t0) REVERT: A 41 LYS cc_start: 0.8615 (mppt) cc_final: 0.8390 (mmtp) REVERT: A 106 ASP cc_start: 0.7676 (t70) cc_final: 0.7308 (m-30) REVERT: D 110 PHE cc_start: 0.8725 (t80) cc_final: 0.8339 (t80) REVERT: D 145 HIS cc_start: 0.7785 (m-70) cc_final: 0.7437 (m-70) REVERT: E 5 TYR cc_start: 0.6017 (t80) cc_final: 0.5799 (t80) REVERT: E 94 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8124 (pt) REVERT: E 105 TYR cc_start: 0.8547 (t80) cc_final: 0.8195 (t80) REVERT: E 110 MET cc_start: 0.7305 (mmp) cc_final: 0.7029 (mmp) REVERT: F 55 GLU cc_start: 0.8688 (pt0) cc_final: 0.8260 (tm-30) REVERT: F 73 ASP cc_start: 0.7155 (t0) cc_final: 0.5423 (t0) REVERT: F 177 MET cc_start: 0.7344 (tmm) cc_final: 0.6903 (tmm) REVERT: G 91 ILE cc_start: 0.3862 (mp) cc_final: 0.3409 (mt) REVERT: H 102 LEU cc_start: 0.8625 (tt) cc_final: 0.8293 (tp) outliers start: 33 outliers final: 20 residues processed: 161 average time/residue: 0.2117 time to fit residues: 49.5470 Evaluate side-chains 143 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 83 HIS ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.063642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.054059 restraints weight = 73492.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.055459 restraints weight = 49463.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.056476 restraints weight = 36652.312| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10683 Z= 0.177 Angle : 0.728 9.025 14450 Z= 0.381 Chirality : 0.046 0.255 1631 Planarity : 0.005 0.070 1849 Dihedral : 6.821 84.126 1405 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.46 % Allowed : 18.18 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.23), residues: 1274 helix: 0.02 (0.22), residues: 524 sheet: -1.27 (0.40), residues: 190 loop : -2.25 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 94 HIS 0.012 0.002 HIS F 169 PHE 0.030 0.002 PHE F 39 TYR 0.025 0.002 TYR E 114 ARG 0.018 0.001 ARG F 59 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 496) hydrogen bonds : angle 5.71338 ( 1425) covalent geometry : bond 0.00393 (10683) covalent geometry : angle 0.72822 (14450) *********************** 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 186 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8356 (t0) cc_final: 0.7961 (t0) REVERT: A 41 LYS cc_start: 0.8712 (mppt) cc_final: 0.8457 (mmtp) REVERT: B 106 LEU cc_start: 0.7888 (mt) cc_final: 0.7646 (mt) REVERT: D 110 PHE cc_start: 0.8737 (t80) cc_final: 0.8341 (t80) REVERT: E 94 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8198 (pt) REVERT: E 105 TYR cc_start: 0.8634 (t80) cc_final: 0.8287 (t80) REVERT: F 55 GLU cc_start: 0.8689 (pt0) cc_final: 0.8204 (tm-30) REVERT: F 177 MET cc_start: 0.7287 (tmm) cc_final: 0.6985 (tmm) REVERT: G 91 ILE cc_start: 0.4065 (mp) cc_final: 0.3619 (mt) outliers start: 52 outliers final: 29 residues processed: 172 average time/residue: 0.2514 time to fit residues: 62.9371 Evaluate side-chains 150 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS C 22 ASN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.064806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.055051 restraints weight = 74503.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.056466 restraints weight = 50164.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.057490 restraints weight = 37145.725| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10683 Z= 0.148 Angle : 0.694 8.522 14450 Z= 0.363 Chirality : 0.045 0.176 1631 Planarity : 0.005 0.071 1849 Dihedral : 6.647 83.595 1405 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 4.46 % Allowed : 19.38 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.23), residues: 1274 helix: 0.18 (0.22), residues: 523 sheet: -1.24 (0.39), residues: 193 loop : -2.15 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.006 0.001 HIS F 113 PHE 0.018 0.002 PHE B 35 TYR 0.027 0.002 TYR F 75 ARG 0.017 0.001 ARG F 59 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 496) hydrogen bonds : angle 5.50389 ( 1425) covalent geometry : bond 0.00328 (10683) covalent geometry : angle 0.69388 (14450) *********************** 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 185 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8287 (t0) cc_final: 0.7754 (t0) REVERT: A 41 LYS cc_start: 0.8680 (mppt) cc_final: 0.8385 (mmtp) REVERT: A 106 ASP cc_start: 0.7650 (t70) cc_final: 0.7340 (m-30) REVERT: B 106 LEU cc_start: 0.7691 (mt) cc_final: 0.7481 (mt) REVERT: D 1 MET cc_start: 0.6394 (tpp) cc_final: 0.6030 (tpp) REVERT: D 110 PHE cc_start: 0.8705 (t80) cc_final: 0.8311 (t80) REVERT: D 153 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8462 (mm) REVERT: E 5 TYR cc_start: 0.6058 (t80) cc_final: 0.5626 (t80) REVERT: E 50 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8688 (pm20) REVERT: E 94 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8093 (pt) REVERT: E 105 TYR cc_start: 0.8528 (t80) cc_final: 0.8167 (t80) REVERT: F 55 GLU cc_start: 0.8595 (pt0) cc_final: 0.8172 (tm-30) REVERT: F 73 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.4952 (t0) REVERT: F 177 MET cc_start: 0.7099 (tmm) cc_final: 0.6673 (tmm) REVERT: G 91 ILE cc_start: 0.3927 (mp) cc_final: 0.3427 (mt) REVERT: H 3 PHE cc_start: 0.7422 (m-10) cc_final: 0.7174 (m-10) outliers start: 52 outliers final: 29 residues processed: 169 average time/residue: 0.2638 time to fit residues: 64.8230 Evaluate side-chains 155 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 81 optimal weight: 0.0270 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN B 77 ASN ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 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 = 0.4117 r_free = 0.4117 target = 0.065462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.055670 restraints weight = 72604.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.057100 restraints weight = 48684.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.058118 restraints weight = 36053.681| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10683 Z= 0.135 Angle : 0.678 9.722 14450 Z= 0.352 Chirality : 0.044 0.160 1631 Planarity : 0.004 0.070 1849 Dihedral : 6.277 81.759 1405 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.20 % Allowed : 20.24 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.24), residues: 1274 helix: 0.40 (0.22), residues: 524 sheet: -1.23 (0.39), residues: 188 loop : -2.06 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.006 0.001 HIS E 86 PHE 0.029 0.002 PHE F 39 TYR 0.021 0.002 TYR F 75 ARG 0.004 0.000 ARG G 76 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 496) hydrogen bonds : angle 5.30163 ( 1425) covalent geometry : bond 0.00299 (10683) covalent geometry : angle 0.67842 (14450) *********************** 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 191 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7229 (mmt) cc_final: 0.6952 (mmt) REVERT: A 32 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7877 (t0) REVERT: A 35 ASN cc_start: 0.8390 (t0) cc_final: 0.7891 (t0) REVERT: A 41 LYS cc_start: 0.8724 (mppt) cc_final: 0.8425 (mmtp) REVERT: A 106 ASP cc_start: 0.7699 (t70) cc_final: 0.7397 (m-30) REVERT: A 113 PHE cc_start: 0.4776 (t80) cc_final: 0.3929 (t80) REVERT: B 23 LYS cc_start: 0.5951 (OUTLIER) cc_final: 0.5731 (tmtt) REVERT: B 106 LEU cc_start: 0.7665 (mt) cc_final: 0.7456 (mt) REVERT: D 1 MET cc_start: 0.6417 (tpp) cc_final: 0.6119 (tpp) REVERT: D 110 PHE cc_start: 0.8711 (t80) cc_final: 0.8311 (t80) REVERT: D 153 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8502 (mm) REVERT: E 5 TYR cc_start: 0.6222 (t80) cc_final: 0.5792 (t80) REVERT: E 50 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8776 (pm20) REVERT: E 105 TYR cc_start: 0.8614 (t80) cc_final: 0.8272 (t80) REVERT: E 110 MET cc_start: 0.7425 (mmp) cc_final: 0.7043 (mmp) REVERT: F 55 GLU cc_start: 0.8672 (pt0) cc_final: 0.8241 (tm-30) REVERT: F 73 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.5303 (t0) REVERT: F 177 MET cc_start: 0.7126 (tmm) cc_final: 0.6550 (tmm) REVERT: G 91 ILE cc_start: 0.3914 (mp) cc_final: 0.3417 (mt) outliers start: 49 outliers final: 36 residues processed: 176 average time/residue: 0.1967 time to fit residues: 51.7399 Evaluate side-chains 165 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 60 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.065155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.055393 restraints weight = 73407.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.056814 restraints weight = 49030.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.057861 restraints weight = 36105.511| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10683 Z= 0.142 Angle : 0.685 8.787 14450 Z= 0.356 Chirality : 0.045 0.279 1631 Planarity : 0.005 0.069 1849 Dihedral : 6.229 80.351 1405 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.63 % Allowed : 21.70 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.24), residues: 1274 helix: 0.47 (0.22), residues: 524 sheet: -1.22 (0.38), residues: 190 loop : -2.01 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.005 0.001 HIS H 66 PHE 0.033 0.002 PHE D 17 TYR 0.020 0.002 TYR C 69 ARG 0.004 0.000 ARG G 76 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 496) hydrogen bonds : angle 5.28694 ( 1425) covalent geometry : bond 0.00319 (10683) covalent geometry : angle 0.68513 (14450) *********************** 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 183 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7882 (t0) REVERT: A 35 ASN cc_start: 0.8374 (t0) cc_final: 0.7775 (t0) REVERT: A 41 LYS cc_start: 0.8766 (mppt) cc_final: 0.8451 (mmtp) REVERT: A 106 ASP cc_start: 0.7724 (t70) cc_final: 0.7401 (m-30) REVERT: A 113 PHE cc_start: 0.4764 (t80) cc_final: 0.3891 (t80) REVERT: A 139 MET cc_start: 0.7919 (mmm) cc_final: 0.7698 (mmm) REVERT: B 86 TYR cc_start: 0.4819 (OUTLIER) cc_final: 0.4301 (p90) REVERT: B 106 LEU cc_start: 0.7708 (mt) cc_final: 0.7496 (mt) REVERT: D 1 MET cc_start: 0.6475 (tpp) cc_final: 0.6251 (tpp) REVERT: D 110 PHE cc_start: 0.8712 (t80) cc_final: 0.8315 (t80) REVERT: D 153 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8548 (mm) REVERT: E 5 TYR cc_start: 0.6318 (t80) cc_final: 0.5831 (t80) REVERT: E 84 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8373 (mm) REVERT: E 105 TYR cc_start: 0.8586 (t80) cc_final: 0.8200 (t80) REVERT: F 55 GLU cc_start: 0.8682 (pt0) cc_final: 0.8235 (tm-30) REVERT: F 73 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.4843 (t0) REVERT: G 91 ILE cc_start: 0.3932 (mp) cc_final: 0.3456 (mt) outliers start: 54 outliers final: 37 residues processed: 170 average time/residue: 0.2036 time to fit residues: 51.3138 Evaluate side-chains 165 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 131 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 95 optimal weight: 0.0670 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.064526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.055015 restraints weight = 74210.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.056408 restraints weight = 49733.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.057419 restraints weight = 36810.257| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10683 Z= 0.165 Angle : 0.734 13.139 14450 Z= 0.379 Chirality : 0.045 0.259 1631 Planarity : 0.005 0.068 1849 Dihedral : 6.326 80.365 1405 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.46 % Allowed : 21.53 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.24), residues: 1274 helix: 0.43 (0.23), residues: 524 sheet: -1.19 (0.38), residues: 195 loop : -2.00 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 147 HIS 0.004 0.001 HIS F 113 PHE 0.035 0.002 PHE F 39 TYR 0.041 0.002 TYR F 75 ARG 0.005 0.001 ARG G 76 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 496) hydrogen bonds : angle 5.37414 ( 1425) covalent geometry : bond 0.00371 (10683) covalent geometry : angle 0.73384 (14450) *********************** 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 175 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7405 (mmt) cc_final: 0.7164 (mmt) REVERT: A 32 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7870 (t0) REVERT: A 35 ASN cc_start: 0.8388 (t0) cc_final: 0.7739 (t0) REVERT: A 41 LYS cc_start: 0.8831 (mppt) cc_final: 0.8487 (mmtp) REVERT: A 113 PHE cc_start: 0.4930 (t80) cc_final: 0.4165 (t80) REVERT: A 142 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7253 (mt) REVERT: B 86 TYR cc_start: 0.4955 (OUTLIER) cc_final: 0.4401 (p90) REVERT: B 106 LEU cc_start: 0.7701 (mt) cc_final: 0.7491 (mt) REVERT: D 110 PHE cc_start: 0.8693 (t80) cc_final: 0.8298 (t80) REVERT: E 5 TYR cc_start: 0.6341 (t80) cc_final: 0.5980 (t80) REVERT: E 105 TYR cc_start: 0.8628 (t80) cc_final: 0.8247 (t80) REVERT: F 55 GLU cc_start: 0.8658 (pt0) cc_final: 0.8213 (tm-30) outliers start: 52 outliers final: 45 residues processed: 162 average time/residue: 0.1863 time to fit residues: 45.2414 Evaluate side-chains 166 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 131 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN B 77 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.065392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.055467 restraints weight = 75687.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.056894 restraints weight = 51083.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.057889 restraints weight = 37979.269| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3483 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= 0.142 Angle : 0.712 11.015 14450 Z= 0.367 Chirality : 0.045 0.241 1631 Planarity : 0.005 0.071 1849 Dihedral : 6.207 79.512 1405 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.55 % Allowed : 21.53 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.24), residues: 1274 helix: 0.50 (0.23), residues: 524 sheet: -1.08 (0.38), residues: 194 loop : -1.95 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 147 HIS 0.004 0.001 HIS H 66 PHE 0.020 0.002 PHE D 119 TYR 0.036 0.002 TYR F 75 ARG 0.004 0.000 ARG G 76 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 496) hydrogen bonds : angle 5.26254 ( 1425) covalent geometry : bond 0.00316 (10683) covalent geometry : angle 0.71214 (14450) *********************** 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 180 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7366 (mmt) cc_final: 0.7141 (mmt) REVERT: A 32 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7874 (t0) REVERT: A 35 ASN cc_start: 0.8341 (t0) cc_final: 0.7796 (t0) REVERT: A 41 LYS cc_start: 0.8684 (mppt) cc_final: 0.8402 (mmtp) REVERT: A 106 ASP cc_start: 0.7644 (t70) cc_final: 0.7381 (m-30) REVERT: A 113 PHE cc_start: 0.4960 (t80) cc_final: 0.4070 (t80) REVERT: A 142 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7199 (mt) REVERT: B 86 TYR cc_start: 0.4998 (OUTLIER) cc_final: 0.4401 (p90) REVERT: B 106 LEU cc_start: 0.7543 (mt) cc_final: 0.7335 (mt) REVERT: D 110 PHE cc_start: 0.8681 (t80) cc_final: 0.8287 (t80) REVERT: E 5 TYR cc_start: 0.6259 (t80) cc_final: 0.5917 (t80) REVERT: E 105 TYR cc_start: 0.8564 (t80) cc_final: 0.8219 (t80) REVERT: E 110 MET cc_start: 0.7545 (mmp) cc_final: 0.6025 (mmm) REVERT: F 55 GLU cc_start: 0.8620 (pt0) cc_final: 0.8181 (tm-30) outliers start: 53 outliers final: 46 residues processed: 169 average time/residue: 0.1970 time to fit residues: 49.5502 Evaluate side-chains 166 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 131 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.065126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.055192 restraints weight = 75447.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.056632 restraints weight = 50830.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.057680 restraints weight = 37810.137| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3577 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= 0.147 Angle : 0.723 10.290 14450 Z= 0.374 Chirality : 0.046 0.305 1631 Planarity : 0.005 0.070 1849 Dihedral : 6.199 79.031 1405 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.12 % Allowed : 21.70 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1274 helix: 0.48 (0.23), residues: 524 sheet: -1.10 (0.38), residues: 195 loop : -1.94 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 147 HIS 0.005 0.001 HIS D 28 PHE 0.046 0.002 PHE F 39 TYR 0.033 0.002 TYR F 75 ARG 0.004 0.000 ARG G 76 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 496) hydrogen bonds : angle 5.26795 ( 1425) covalent geometry : bond 0.00330 (10683) covalent geometry : angle 0.72338 (14450) ********************** 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 167 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7337 (mmt) cc_final: 0.7124 (mmt) REVERT: A 32 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7913 (t0) REVERT: A 35 ASN cc_start: 0.8342 (t0) cc_final: 0.7713 (t0) REVERT: A 41 LYS cc_start: 0.8688 (mppt) cc_final: 0.8373 (mmtp) REVERT: A 82 ARG cc_start: 0.8105 (ttm110) cc_final: 0.7715 (ttm-80) REVERT: A 106 ASP cc_start: 0.7733 (t70) cc_final: 0.7404 (m-30) REVERT: A 113 PHE cc_start: 0.4996 (t80) cc_final: 0.4122 (t80) REVERT: A 142 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7166 (mt) REVERT: B 86 TYR cc_start: 0.4547 (OUTLIER) cc_final: 0.3958 (p90) REVERT: B 106 LEU cc_start: 0.7623 (mt) cc_final: 0.7408 (mt) REVERT: D 110 PHE cc_start: 0.8711 (t80) cc_final: 0.8313 (t80) REVERT: E 5 TYR cc_start: 0.6343 (t80) cc_final: 0.5993 (t80) REVERT: E 105 TYR cc_start: 0.8654 (t80) cc_final: 0.8276 (t80) REVERT: E 110 MET cc_start: 0.6543 (mmp) cc_final: 0.5780 (mmm) REVERT: F 55 GLU cc_start: 0.8709 (pt0) cc_final: 0.8279 (tm-30) REVERT: F 145 CYS cc_start: 0.6360 (t) cc_final: 0.5816 (t) outliers start: 48 outliers final: 43 residues processed: 157 average time/residue: 0.1968 time to fit residues: 46.6879 Evaluate side-chains 163 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 131 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 112 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.065471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.055787 restraints weight = 71922.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.057208 restraints weight = 48195.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.058228 restraints weight = 35626.037| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10683 Z= 0.138 Angle : 0.712 10.032 14450 Z= 0.368 Chirality : 0.046 0.247 1631 Planarity : 0.005 0.071 1849 Dihedral : 6.095 77.241 1405 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.37 % Allowed : 21.87 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.24), residues: 1274 helix: 0.54 (0.23), residues: 524 sheet: -0.97 (0.38), residues: 190 loop : -1.93 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.005 0.001 HIS E 86 PHE 0.019 0.002 PHE B 35 TYR 0.031 0.002 TYR F 75 ARG 0.004 0.000 ARG G 76 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 496) hydrogen bonds : angle 5.19898 ( 1425) covalent geometry : bond 0.00306 (10683) covalent geometry : angle 0.71185 (14450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4803.33 seconds wall clock time: 87 minutes 5.53 seconds (5225.53 seconds total)