Starting phenix.real_space_refine on Fri Sep 11 00:14:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y9a_10734/09_2026/6y9a_10734.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y9a_10734/09_2026/6y9a_10734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y9a_10734/09_2026/6y9a_10734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y9a_10734/09_2026/6y9a_10734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y9a_10734/09_2026/6y9a_10734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y9a_10734/09_2026/6y9a_10734.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 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 41 5.16 5 C 3829 2.51 5 N 965 2.21 5 O 1113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5948 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "B" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1644 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1684 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Time building chain proxies: 1.14, per 1000 atoms: 0.19 Number of scatterers: 5948 At special positions: 0 Unit cell: (61.864, 70.004, 154.66, 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 41 16.00 O 1113 8.00 N 965 7.00 C 3829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 237.3 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 37.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 45 through 51 removed outlier: 5.150A pdb=" N LYS A 50 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 71 Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.617A pdb=" N THR A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 84' Processing helix chain 'A' and resid 85 through 103 removed outlier: 3.865A pdb=" N TRP A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 143 removed outlier: 3.917A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 171 through 176 removed outlier: 4.401A pdb=" N ASN A 176 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 210 Processing helix chain 'B' and resid 45 through 51 removed outlier: 5.825A pdb=" N LYS B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 71 Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.646A pdb=" N VAL B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 100 removed outlier: 4.051A pdb=" N TRP B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 143 removed outlier: 3.710A pdb=" N LYS B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 171 through 176 removed outlier: 4.078A pdb=" N ASN B 176 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 212 removed outlier: 3.585A pdb=" N GLN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'L' and resid 126 through 133 Processing helix chain 'L' and resid 188 through 193 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.723A pdb=" N LYS H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP H 59 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 19 through 21 removed outlier: 3.900A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET H 81 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR H 80 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.563A pdb=" N LEU H 130 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.635A pdb=" N THR H 157 " --> pdb=" O ASN H 205 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 204 " --> pdb=" O VAL H 213 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL H 213 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.739A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER L 22 " --> pdb=" O THR L 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.572A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR L 39 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.572A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN L 95 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 68 through 71 Processing sheet with id=AB1, first strand: chain 'L' and resid 120 through 123 removed outlier: 3.646A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU L 184 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS L 139 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 182 " --> pdb=" O CYS L 139 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU L 141 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.972A pdb=" N LYS L 150 " --> pdb=" O THR L 202 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR L 202 " --> pdb=" O LYS L 150 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN L 152 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 200 " --> pdb=" O GLN L 152 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS L 154 " --> pdb=" O ALA L 198 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR L 197 " --> pdb=" O PHE L 214 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE L 214 " --> pdb=" O TYR L 197 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS L 212 " --> pdb=" O CYS L 199 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL L 210 " --> pdb=" O VAL L 201 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 717 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: 0.83 Time building geometry restraints manager: 0.61 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: 1839 1.34 - 1.46: 1465 1.46 - 1.58: 2714 1.58 - 1.70: 2 1.70 - 1.82: 65 Bond restraints: 6085 Sorted by residual: bond pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.61e+00 bond pdb=" CB PRO A 73 " pdb=" CG PRO A 73 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.70e+00 bond pdb=" CG1 ILE A 141 " pdb=" CD1 ILE A 141 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.50e+00 bond pdb=" CA THR B 180 " pdb=" C THR B 180 " ideal model delta sigma weight residual 1.520 1.504 0.015 1.40e-02 5.10e+03 1.21e+00 bond pdb=" N PRO B 73 " pdb=" CA PRO B 73 " ideal model delta sigma weight residual 1.469 1.482 -0.013 1.28e-02 6.10e+03 1.10e+00 ... (remaining 6080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 7992 2.04 - 4.09: 221 4.09 - 6.13: 35 6.13 - 8.18: 7 8.18 - 10.22: 2 Bond angle restraints: 8257 Sorted by residual: angle pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 112.00 105.14 6.86 1.40e+00 5.10e-01 2.40e+01 angle pdb=" CA PRO A 73 " pdb=" N PRO A 73 " pdb=" CD PRO A 73 " ideal model delta sigma weight residual 112.00 105.64 6.36 1.40e+00 5.10e-01 2.06e+01 angle pdb=" N LYS B 148 " pdb=" CA LYS B 148 " pdb=" C LYS B 148 " ideal model delta sigma weight residual 111.03 115.64 -4.61 1.11e+00 8.12e-01 1.73e+01 angle pdb=" N GLN A 181 " pdb=" CA GLN A 181 " pdb=" C GLN A 181 " ideal model delta sigma weight residual 111.28 106.77 4.51 1.09e+00 8.42e-01 1.71e+01 angle pdb=" N GLN B 181 " pdb=" CA GLN B 181 " pdb=" C GLN B 181 " ideal model delta sigma weight residual 111.28 107.01 4.27 1.09e+00 8.42e-01 1.54e+01 ... (remaining 8252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 3284 17.24 - 34.48: 278 34.48 - 51.72: 61 51.72 - 68.96: 10 68.96 - 86.20: 7 Dihedral angle restraints: 3640 sinusoidal: 1404 harmonic: 2236 Sorted by residual: dihedral pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " pdb=" SG CYS L 199 " pdb=" CB CYS L 199 " ideal model delta sinusoidal sigma weight residual 93.00 176.92 -83.92 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS H 146 " pdb=" SG CYS H 146 " pdb=" SG CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sinusoidal sigma weight residual 93.00 16.07 76.93 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 18.32 74.68 1 1.00e+01 1.00e-02 7.06e+01 ... (remaining 3637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 750 0.058 - 0.116: 171 0.116 - 0.175: 20 0.175 - 0.233: 3 0.233 - 0.291: 1 Chirality restraints: 945 Sorted by residual: chirality pdb=" CG LEU B 122 " pdb=" CB LEU B 122 " pdb=" CD1 LEU B 122 " pdb=" CD2 LEU B 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB VAL H 190 " pdb=" CA VAL H 190 " pdb=" CG1 VAL H 190 " pdb=" CG2 VAL H 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLN L 55 " pdb=" N GLN L 55 " pdb=" C GLN L 55 " pdb=" CB GLN L 55 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 942 not shown) Planarity restraints: 1030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 179 " 0.031 2.00e-02 2.50e+03 6.11e-02 3.73e+01 pdb=" C SER B 179 " -0.106 2.00e-02 2.50e+03 pdb=" O SER B 179 " 0.038 2.00e-02 2.50e+03 pdb=" N THR B 180 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 179 " -0.028 2.00e-02 2.50e+03 5.47e-02 3.00e+01 pdb=" C SER A 179 " 0.095 2.00e-02 2.50e+03 pdb=" O SER A 179 " -0.035 2.00e-02 2.50e+03 pdb=" N THR A 180 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 116 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.69e+01 pdb=" C LYS B 116 " 0.090 2.00e-02 2.50e+03 pdb=" O LYS B 116 " -0.034 2.00e-02 2.50e+03 pdb=" N MET B 117 " -0.030 2.00e-02 2.50e+03 ... (remaining 1027 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 566 2.75 - 3.29: 6136 3.29 - 3.82: 9405 3.82 - 4.36: 10399 4.36 - 4.90: 17289 Nonbonded interactions: 43795 Sorted by model distance: nonbonded pdb=" O GLY H 103 " pdb=" OH TYR L 39 " model vdw 2.211 3.040 nonbonded pdb=" O TYR L 191 " pdb=" OH TYR L 197 " model vdw 2.271 3.040 nonbonded pdb=" O HIS L 194 " pdb=" NH2 ARG L 216 " model vdw 2.281 3.120 nonbonded pdb=" OG1 THR H 199 " pdb=" OE2 GLU H 218 " model vdw 2.312 3.040 nonbonded pdb=" ND2 ASN A 163 " pdb=" OD1 ASN A 166 " model vdw 2.328 3.120 ... (remaining 43790 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 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4435 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 : 0.004 0.107 6091 Z= 0.153 Angle : 0.809 10.221 8269 Z= 0.443 Chirality : 0.050 0.291 945 Planarity : 0.008 0.127 1030 Dihedral : 13.593 86.201 2192 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.29), residues: 766 helix: -0.51 (0.30), residues: 228 sheet: 0.10 (0.38), residues: 174 loop : -1.35 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 98 TYR 0.014 0.001 TYR L 197 PHE 0.040 0.002 PHE B 62 TRP 0.026 0.001 TRP H 109 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6085) covalent geometry : angle 0.80880 / 0.44 ( 8257) SS BOND : bond 0.00433 / 0.21 ( 6) SS BOND : angle 1.14637 / 0.68 ( 12) hydrogen bonds : bond 0.19682 / 12.84 ( 263) hydrogen bonds : angle 6.69154 / 4.63 ( 717) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.4432 (mmm) cc_final: 0.4112 (mmm) REVERT: A 117 MET cc_start: 0.8031 (ptt) cc_final: 0.6041 (tpt) REVERT: B 149 MET cc_start: 0.7266 (mpp) cc_final: 0.6624 (mpp) REVERT: L 42 LEU cc_start: 0.6631 (tt) cc_final: 0.6238 (tt) REVERT: L 56 MET cc_start: 0.7262 (tmm) cc_final: 0.6827 (ppp) REVERT: L 146 PRO cc_start: 0.6978 (Cg_endo) cc_final: 0.6464 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0603 time to fit residues: 15.9247 Evaluate side-chains 155 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.0670 chunk 61 optimal weight: 0.0020 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.3126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN A 204 GLN B 120 ASN H 39 GLN H 161 ASN L 47 GLN L 194 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.158640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.125153 restraints weight = 15276.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.130523 restraints weight = 10311.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.134712 restraints weight = 7449.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.138129 restraints weight = 5675.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.140755 restraints weight = 4476.505| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6091 Z= 0.118 Angle : 0.614 6.730 8269 Z= 0.319 Chirality : 0.044 0.166 945 Planarity : 0.006 0.068 1030 Dihedral : 4.565 19.524 824 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.15 % Allowed : 4.50 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.30), residues: 766 helix: 0.87 (0.33), residues: 241 sheet: 0.74 (0.42), residues: 157 loop : -1.17 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 98 TYR 0.017 0.001 TYR L 54 PHE 0.025 0.001 PHE B 62 TRP 0.025 0.002 TRP H 33 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 6085) covalent geometry : angle 0.61365 / 0.32 ( 8257) SS BOND : bond 0.00346 / 0.17 ( 6) SS BOND : angle 0.84777 / 0.51 ( 12) hydrogen bonds : bond 0.03654 / 2.45 ( 263) hydrogen bonds : angle 4.69859 / 3.30 ( 717) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7775 (ptt) cc_final: 0.6438 (tpt) REVERT: A 119 MET cc_start: 0.8915 (mmp) cc_final: 0.8666 (mmm) REVERT: A 164 ILE cc_start: 0.8035 (mt) cc_final: 0.7760 (mp) REVERT: A 176 ASN cc_start: 0.8068 (m-40) cc_final: 0.7614 (m-40) REVERT: A 190 PHE cc_start: 0.8821 (m-10) cc_final: 0.8469 (m-80) REVERT: B 58 MET cc_start: 0.8730 (ttm) cc_final: 0.8366 (ttt) REVERT: B 62 PHE cc_start: 0.8578 (m-80) cc_final: 0.8150 (m-80) REVERT: B 119 MET cc_start: 0.8513 (tpt) cc_final: 0.8282 (tpt) REVERT: B 131 MET cc_start: 0.7501 (mmp) cc_final: 0.7191 (mmm) REVERT: B 149 MET cc_start: 0.7420 (mpp) cc_final: 0.6744 (mpp) REVERT: B 150 GLU cc_start: 0.7778 (pp20) cc_final: 0.7447 (pp20) REVERT: B 184 TYR cc_start: 0.8228 (m-10) cc_final: 0.7774 (m-10) REVERT: B 211 ILE cc_start: 0.7332 (mm) cc_final: 0.7129 (mm) REVERT: H 22 CYS cc_start: 0.4924 (p) cc_final: 0.4506 (p) REVERT: H 35 ASN cc_start: 0.8647 (p0) cc_final: 0.8367 (p0) REVERT: H 36 TRP cc_start: 0.7933 (m100) cc_final: 0.7434 (m100) REVERT: H 73 ASP cc_start: 0.9290 (t0) cc_final: 0.9000 (t0) REVERT: H 99 ASN cc_start: 0.8136 (t0) cc_final: 0.7547 (p0) REVERT: H 100 VAL cc_start: 0.8851 (t) cc_final: 0.8263 (t) REVERT: H 128 PHE cc_start: 0.8814 (m-80) cc_final: 0.8601 (m-80) REVERT: H 201 ILE cc_start: 0.8348 (tp) cc_final: 0.8068 (tp) REVERT: L 79 LYS cc_start: 0.7831 (tptt) cc_final: 0.7201 (tppt) REVERT: L 80 ILE cc_start: 0.7033 (mp) cc_final: 0.6620 (mm) REVERT: L 91 TYR cc_start: 0.9074 (m-10) cc_final: 0.8366 (m-80) REVERT: L 123 PHE cc_start: 0.7965 (m-80) cc_final: 0.7573 (m-80) REVERT: L 175 ASP cc_start: 0.8683 (m-30) cc_final: 0.8454 (m-30) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.0547 time to fit residues: 15.0613 Evaluate side-chains 163 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 158 HIS L 47 GLN L 129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.155121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.120421 restraints weight = 14168.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.125673 restraints weight = 9561.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.129905 restraints weight = 6931.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.133343 restraints weight = 5288.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.136008 restraints weight = 4173.139| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6091 Z= 0.107 Angle : 0.574 7.209 8269 Z= 0.296 Chirality : 0.043 0.171 945 Planarity : 0.005 0.058 1030 Dihedral : 4.294 17.507 824 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.15 % Allowed : 3.15 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.30), residues: 766 helix: 1.44 (0.33), residues: 233 sheet: 0.82 (0.39), residues: 175 loop : -1.04 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.016 0.001 TYR L 54 PHE 0.018 0.001 PHE B 62 TRP 0.022 0.002 TRP H 33 HIS 0.007 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 6085) covalent geometry : angle 0.57359 / 0.30 ( 8257) SS BOND : bond 0.00378 / 0.19 ( 6) SS BOND : angle 0.98866 / 0.58 ( 12) hydrogen bonds : bond 0.03453 / 2.31 ( 263) hydrogen bonds : angle 4.34220 / 3.04 ( 717) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8913 (mmp) cc_final: 0.8686 (mmm) REVERT: A 164 ILE cc_start: 0.8096 (mt) cc_final: 0.7775 (mp) REVERT: A 181 GLN cc_start: 0.8948 (mt0) cc_final: 0.8628 (tp40) REVERT: A 190 PHE cc_start: 0.8913 (m-10) cc_final: 0.8499 (m-80) REVERT: B 58 MET cc_start: 0.8660 (ttm) cc_final: 0.8360 (ttt) REVERT: B 62 PHE cc_start: 0.8619 (m-80) cc_final: 0.8181 (m-80) REVERT: B 119 MET cc_start: 0.8513 (tpt) cc_final: 0.8175 (tpt) REVERT: B 140 ASN cc_start: 0.7325 (m110) cc_final: 0.7097 (m110) REVERT: B 149 MET cc_start: 0.7131 (mpp) cc_final: 0.6501 (mpp) REVERT: B 150 GLU cc_start: 0.7579 (pp20) cc_final: 0.7177 (pp20) REVERT: B 161 TYR cc_start: 0.6715 (m-80) cc_final: 0.6327 (m-80) REVERT: B 174 GLU cc_start: 0.9166 (mp0) cc_final: 0.8854 (mp0) REVERT: B 184 TYR cc_start: 0.8290 (m-10) cc_final: 0.7870 (m-10) REVERT: B 211 ILE cc_start: 0.7356 (mm) cc_final: 0.7125 (mm) REVERT: H 22 CYS cc_start: 0.5356 (p) cc_final: 0.4789 (p) REVERT: H 36 TRP cc_start: 0.8270 (m100) cc_final: 0.7661 (m100) REVERT: H 47 TRP cc_start: 0.7090 (t60) cc_final: 0.6764 (t60) REVERT: H 73 ASP cc_start: 0.9291 (t0) cc_final: 0.9017 (t0) REVERT: H 104 TYR cc_start: 0.7363 (m-10) cc_final: 0.7145 (m-10) REVERT: H 201 ILE cc_start: 0.8408 (tp) cc_final: 0.8132 (tp) REVERT: L 76 PHE cc_start: 0.7560 (m-80) cc_final: 0.7014 (m-80) REVERT: L 91 TYR cc_start: 0.9195 (m-10) cc_final: 0.8635 (m-80) REVERT: L 123 PHE cc_start: 0.8257 (m-80) cc_final: 0.7854 (m-80) REVERT: L 175 ASP cc_start: 0.8657 (m-30) cc_final: 0.8410 (m-30) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.0582 time to fit residues: 15.3568 Evaluate side-chains 154 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 70 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 chunk 61 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 120 ASN L 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.153771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.118892 restraints weight = 14205.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.124164 restraints weight = 9630.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.128244 restraints weight = 7012.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.131684 restraints weight = 5347.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.134287 restraints weight = 4234.971| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6091 Z= 0.102 Angle : 0.563 7.271 8269 Z= 0.288 Chirality : 0.042 0.169 945 Planarity : 0.005 0.056 1030 Dihedral : 4.177 16.954 824 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.30), residues: 766 helix: 1.86 (0.33), residues: 237 sheet: 0.89 (0.38), residues: 181 loop : -0.90 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.014 0.001 TYR L 54 PHE 0.015 0.001 PHE B 62 TRP 0.016 0.001 TRP H 33 HIS 0.002 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 6085) covalent geometry : angle 0.56241 / 0.29 ( 8257) SS BOND : bond 0.00406 / 0.25 ( 6) SS BOND : angle 0.94520 / 0.54 ( 12) hydrogen bonds : bond 0.03346 / 2.27 ( 263) hydrogen bonds : angle 4.08532 / 2.88 ( 717) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8958 (mmp) cc_final: 0.8724 (mmm) REVERT: A 164 ILE cc_start: 0.8137 (mt) cc_final: 0.7900 (mp) REVERT: A 176 ASN cc_start: 0.8340 (m-40) cc_final: 0.7996 (m-40) REVERT: A 181 GLN cc_start: 0.8974 (mt0) cc_final: 0.8653 (tp40) REVERT: A 190 PHE cc_start: 0.8963 (m-10) cc_final: 0.8679 (m-80) REVERT: B 58 MET cc_start: 0.8680 (ttm) cc_final: 0.8298 (ttt) REVERT: B 62 PHE cc_start: 0.8595 (m-80) cc_final: 0.8155 (m-80) REVERT: B 119 MET cc_start: 0.8327 (tpt) cc_final: 0.8113 (tpt) REVERT: B 131 MET cc_start: 0.7308 (mmm) cc_final: 0.7072 (mmm) REVERT: B 140 ASN cc_start: 0.7401 (m110) cc_final: 0.7094 (m110) REVERT: B 149 MET cc_start: 0.7140 (mpp) cc_final: 0.6549 (mpp) REVERT: B 150 GLU cc_start: 0.7469 (pp20) cc_final: 0.7044 (pp20) REVERT: B 161 TYR cc_start: 0.6751 (m-80) cc_final: 0.6345 (m-80) REVERT: B 176 ASN cc_start: 0.7837 (m-40) cc_final: 0.7198 (p0) REVERT: B 184 TYR cc_start: 0.8363 (m-10) cc_final: 0.7906 (m-10) REVERT: B 211 ILE cc_start: 0.7427 (mm) cc_final: 0.7184 (mm) REVERT: H 73 ASP cc_start: 0.9340 (t0) cc_final: 0.9061 (t0) REVERT: H 201 ILE cc_start: 0.8430 (tp) cc_final: 0.8151 (tp) REVERT: L 21 ILE cc_start: 0.7542 (tp) cc_final: 0.7268 (tp) REVERT: L 76 PHE cc_start: 0.7327 (m-80) cc_final: 0.7099 (m-80) REVERT: L 91 TYR cc_start: 0.9095 (m-10) cc_final: 0.8547 (m-80) REVERT: L 123 PHE cc_start: 0.8341 (m-80) cc_final: 0.7898 (m-80) REVERT: L 175 ASP cc_start: 0.8656 (m-30) cc_final: 0.8417 (m-30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0548 time to fit residues: 14.3558 Evaluate side-chains 156 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 58 optimal weight: 0.0470 chunk 57 optimal weight: 5.9990 chunk 62 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.7648 > 50:) chunk 3 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN L 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.151449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.115709 restraints weight = 14801.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.120887 restraints weight = 9970.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.124938 restraints weight = 7278.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.128211 restraints weight = 5604.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.130832 restraints weight = 4476.980| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6091 Z= 0.104 Angle : 0.567 7.508 8269 Z= 0.288 Chirality : 0.042 0.155 945 Planarity : 0.005 0.056 1030 Dihedral : 4.159 16.171 824 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.31), residues: 766 helix: 1.93 (0.33), residues: 237 sheet: 0.82 (0.38), residues: 181 loop : -0.79 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.013 0.001 TYR L 54 PHE 0.019 0.001 PHE A 203 TRP 0.023 0.002 TRP H 36 HIS 0.002 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 6085) covalent geometry : angle 0.56644 / 0.29 ( 8257) SS BOND : bond 0.00468 / 0.28 ( 6) SS BOND : angle 0.86888 / 0.50 ( 12) hydrogen bonds : bond 0.03277 / 2.19 ( 263) hydrogen bonds : angle 4.02667 / 2.82 ( 717) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8122 (mt) cc_final: 0.7779 (mp) REVERT: A 190 PHE cc_start: 0.8973 (m-10) cc_final: 0.8595 (m-80) REVERT: B 58 MET cc_start: 0.8735 (ttm) cc_final: 0.8356 (ttt) REVERT: B 62 PHE cc_start: 0.8728 (m-80) cc_final: 0.8208 (m-80) REVERT: B 119 MET cc_start: 0.8258 (tpt) cc_final: 0.8017 (tpt) REVERT: B 131 MET cc_start: 0.7365 (mmm) cc_final: 0.7147 (mmm) REVERT: B 140 ASN cc_start: 0.7442 (m110) cc_final: 0.7110 (m110) REVERT: B 149 MET cc_start: 0.6865 (mpp) cc_final: 0.6350 (mpp) REVERT: B 150 GLU cc_start: 0.7414 (pp20) cc_final: 0.7034 (pp20) REVERT: B 176 ASN cc_start: 0.7799 (m-40) cc_final: 0.7146 (p0) REVERT: B 184 TYR cc_start: 0.8358 (m-10) cc_final: 0.7936 (m-10) REVERT: B 211 ILE cc_start: 0.7395 (mm) cc_final: 0.7137 (mm) REVERT: H 36 TRP cc_start: 0.8315 (m100) cc_final: 0.8097 (m-10) REVERT: H 73 ASP cc_start: 0.9302 (t0) cc_final: 0.9049 (t0) REVERT: H 128 PHE cc_start: 0.8388 (m-80) cc_final: 0.8030 (m-80) REVERT: H 150 ASP cc_start: 0.7171 (m-30) cc_final: 0.6938 (m-30) REVERT: L 76 PHE cc_start: 0.7729 (m-80) cc_final: 0.7269 (m-80) REVERT: L 91 TYR cc_start: 0.9082 (m-10) cc_final: 0.8634 (m-80) REVERT: L 123 PHE cc_start: 0.8518 (m-80) cc_final: 0.8053 (m-80) REVERT: L 175 ASP cc_start: 0.8703 (m-30) cc_final: 0.8460 (m-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0523 time to fit residues: 13.4330 Evaluate side-chains 152 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 145 HIS L 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.137230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.103656 restraints weight = 16021.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.108613 restraints weight = 10685.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.112338 restraints weight = 7742.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.115205 restraints weight = 5970.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.117336 restraints weight = 4814.680| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6091 Z= 0.157 Angle : 0.620 7.327 8269 Z= 0.324 Chirality : 0.044 0.150 945 Planarity : 0.005 0.054 1030 Dihedral : 4.520 17.223 824 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.31), residues: 766 helix: 1.35 (0.32), residues: 257 sheet: 0.41 (0.36), residues: 195 loop : -0.72 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 24 TYR 0.016 0.002 TYR L 54 PHE 0.015 0.002 PHE L 76 TRP 0.020 0.002 TRP B 89 HIS 0.005 0.001 HIS L 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 6085) covalent geometry : angle 0.61862 / 0.32 ( 8257) SS BOND : bond 0.00350 / 0.16 ( 6) SS BOND : angle 1.32953 / 0.77 ( 12) hydrogen bonds : bond 0.03794 / 2.60 ( 263) hydrogen bonds : angle 4.20557 / 2.96 ( 717) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8274 (mt) cc_final: 0.7991 (mp) REVERT: A 190 PHE cc_start: 0.9238 (m-10) cc_final: 0.8923 (m-80) REVERT: B 119 MET cc_start: 0.8432 (tpt) cc_final: 0.8175 (tpt) REVERT: B 131 MET cc_start: 0.7851 (mmm) cc_final: 0.7623 (mmm) REVERT: B 140 ASN cc_start: 0.7810 (m110) cc_final: 0.7534 (m110) REVERT: B 149 MET cc_start: 0.6763 (mpp) cc_final: 0.6230 (mpp) REVERT: B 150 GLU cc_start: 0.7360 (pp20) cc_final: 0.6863 (pp20) REVERT: B 161 TYR cc_start: 0.7318 (m-80) cc_final: 0.7017 (m-80) REVERT: B 176 ASN cc_start: 0.7929 (m-40) cc_final: 0.7338 (p0) REVERT: B 184 TYR cc_start: 0.8345 (m-10) cc_final: 0.7898 (m-10) REVERT: B 187 GLN cc_start: 0.8741 (mt0) cc_final: 0.8484 (mt0) REVERT: H 3 GLN cc_start: 0.8340 (mp10) cc_final: 0.8103 (mp10) REVERT: H 47 TRP cc_start: 0.8685 (t60) cc_final: 0.8473 (t60) REVERT: H 73 ASP cc_start: 0.9320 (t0) cc_final: 0.9065 (t0) REVERT: H 94 TYR cc_start: 0.8387 (m-80) cc_final: 0.7643 (m-80) REVERT: L 70 SER cc_start: 0.8783 (p) cc_final: 0.8205 (p) REVERT: L 76 PHE cc_start: 0.7843 (m-80) cc_final: 0.7625 (m-80) REVERT: L 91 TYR cc_start: 0.8841 (m-10) cc_final: 0.8313 (m-80) REVERT: L 98 GLU cc_start: 0.9156 (pt0) cc_final: 0.8776 (pm20) REVERT: L 175 ASP cc_start: 0.8741 (m-30) cc_final: 0.8521 (m-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0520 time to fit residues: 13.2785 Evaluate side-chains 147 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 ASN L 47 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.139333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.105865 restraints weight = 14713.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.110962 restraints weight = 9623.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.114873 restraints weight = 6937.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.118013 restraints weight = 5301.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.120455 restraints weight = 4214.361| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6091 Z= 0.113 Angle : 0.605 6.541 8269 Z= 0.309 Chirality : 0.044 0.177 945 Planarity : 0.005 0.054 1030 Dihedral : 4.336 16.251 824 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.31), residues: 766 helix: 1.62 (0.33), residues: 245 sheet: 0.46 (0.37), residues: 187 loop : -0.68 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.013 0.001 TYR L 54 PHE 0.018 0.002 PHE A 203 TRP 0.026 0.002 TRP H 33 HIS 0.002 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6085) covalent geometry : angle 0.60391 / 0.31 ( 8257) SS BOND : bond 0.00320 / 0.16 ( 6) SS BOND : angle 0.93345 / 0.49 ( 12) hydrogen bonds : bond 0.03518 / 2.35 ( 263) hydrogen bonds : angle 4.10151 / 2.90 ( 717) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.8610 (t80) cc_final: 0.8262 (t80) REVERT: A 164 ILE cc_start: 0.8260 (mt) cc_final: 0.8019 (mp) REVERT: A 171 ASN cc_start: 0.9302 (p0) cc_final: 0.9076 (p0) REVERT: A 190 PHE cc_start: 0.9191 (m-10) cc_final: 0.8869 (m-80) REVERT: B 131 MET cc_start: 0.7799 (mmm) cc_final: 0.7585 (mmm) REVERT: B 140 ASN cc_start: 0.7862 (m110) cc_final: 0.7491 (m110) REVERT: B 149 MET cc_start: 0.6770 (mpp) cc_final: 0.6237 (mpp) REVERT: B 150 GLU cc_start: 0.7382 (pp20) cc_final: 0.6950 (pp20) REVERT: B 161 TYR cc_start: 0.7792 (m-80) cc_final: 0.7180 (m-80) REVERT: B 176 ASN cc_start: 0.7942 (m-40) cc_final: 0.7265 (p0) REVERT: B 184 TYR cc_start: 0.8362 (m-10) cc_final: 0.7885 (m-10) REVERT: B 187 GLN cc_start: 0.8746 (mt0) cc_final: 0.8522 (mt0) REVERT: H 3 GLN cc_start: 0.8333 (mp10) cc_final: 0.8113 (mp10) REVERT: H 47 TRP cc_start: 0.8810 (t60) cc_final: 0.7815 (t60) REVERT: H 73 ASP cc_start: 0.9307 (t0) cc_final: 0.9032 (t0) REVERT: H 94 TYR cc_start: 0.8372 (m-80) cc_final: 0.7438 (m-80) REVERT: H 128 PHE cc_start: 0.8551 (m-80) cc_final: 0.8183 (m-80) REVERT: L 21 ILE cc_start: 0.7858 (tp) cc_final: 0.7629 (tp) REVERT: L 70 SER cc_start: 0.8711 (p) cc_final: 0.8213 (p) REVERT: L 76 PHE cc_start: 0.8042 (m-80) cc_final: 0.7757 (m-80) REVERT: L 91 TYR cc_start: 0.8801 (m-10) cc_final: 0.8212 (m-80) REVERT: L 98 GLU cc_start: 0.9188 (pt0) cc_final: 0.8910 (pm20) REVERT: L 175 ASP cc_start: 0.8762 (m-30) cc_final: 0.8540 (m-30) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0520 time to fit residues: 13.6328 Evaluate side-chains 146 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 0.0870 chunk 44 optimal weight: 0.0370 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 61 optimal weight: 0.2980 chunk 59 optimal weight: 0.0870 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 ASN L 47 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.143983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.110386 restraints weight = 15597.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.115700 restraints weight = 10341.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.119806 restraints weight = 7489.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.122980 restraints weight = 5735.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.125393 restraints weight = 4565.693| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6091 Z= 0.111 Angle : 0.619 6.984 8269 Z= 0.312 Chirality : 0.044 0.184 945 Planarity : 0.005 0.050 1030 Dihedral : 4.291 15.109 824 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.31), residues: 766 helix: 1.74 (0.33), residues: 245 sheet: 0.39 (0.38), residues: 187 loop : -0.64 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 156 TYR 0.013 0.001 TYR L 191 PHE 0.019 0.002 PHE A 203 TRP 0.028 0.002 TRP L 40 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 6085) covalent geometry : angle 0.61898 / 0.31 ( 8257) SS BOND : bond 0.00443 / 0.29 ( 6) SS BOND : angle 0.75453 / 0.42 ( 12) hydrogen bonds : bond 0.03455 / 2.30 ( 263) hydrogen bonds : angle 3.92879 / 2.78 ( 717) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8220 (mt) cc_final: 0.7883 (mp) REVERT: A 171 ASN cc_start: 0.9259 (p0) cc_final: 0.9047 (p0) REVERT: A 190 PHE cc_start: 0.9124 (m-10) cc_final: 0.8718 (m-80) REVERT: B 131 MET cc_start: 0.7749 (mmm) cc_final: 0.7540 (mmm) REVERT: B 140 ASN cc_start: 0.7834 (m110) cc_final: 0.7440 (m110) REVERT: B 149 MET cc_start: 0.6743 (mpp) cc_final: 0.6240 (mpp) REVERT: B 150 GLU cc_start: 0.7419 (pp20) cc_final: 0.6964 (pp20) REVERT: B 161 TYR cc_start: 0.7462 (m-80) cc_final: 0.7067 (m-80) REVERT: B 176 ASN cc_start: 0.7952 (m-40) cc_final: 0.7203 (p0) REVERT: B 184 TYR cc_start: 0.8357 (m-10) cc_final: 0.7905 (m-10) REVERT: H 47 TRP cc_start: 0.8731 (t60) cc_final: 0.8199 (t60) REVERT: L 4 MET cc_start: 0.5371 (mmm) cc_final: 0.1038 (tpp) REVERT: L 55 GLN cc_start: 0.8689 (mp10) cc_final: 0.8370 (tp-100) REVERT: L 70 SER cc_start: 0.8785 (p) cc_final: 0.8290 (p) REVERT: L 91 TYR cc_start: 0.8890 (m-10) cc_final: 0.8401 (m-80) REVERT: L 95 GLN cc_start: 0.8205 (pt0) cc_final: 0.7326 (pm20) REVERT: L 98 GLU cc_start: 0.9194 (pt0) cc_final: 0.8946 (pm20) REVERT: L 175 ASP cc_start: 0.8764 (m-30) cc_final: 0.8539 (m-30) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.0554 time to fit residues: 14.2861 Evaluate side-chains 154 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 0.0030 chunk 35 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 40 optimal weight: 0.0570 chunk 73 optimal weight: 0.8980 overall best weight: 0.3286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.144247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.110562 restraints weight = 14343.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.115877 restraints weight = 9472.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.120043 restraints weight = 6766.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.123041 restraints weight = 5124.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.125554 restraints weight = 4070.444| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6091 Z= 0.108 Angle : 0.620 8.218 8269 Z= 0.311 Chirality : 0.044 0.170 945 Planarity : 0.005 0.051 1030 Dihedral : 4.209 15.184 824 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.31), residues: 766 helix: 1.76 (0.33), residues: 245 sheet: 0.32 (0.38), residues: 187 loop : -0.61 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.011 0.001 TYR A 86 PHE 0.020 0.002 PHE A 203 TRP 0.035 0.002 TRP L 40 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 6085) covalent geometry : angle 0.61949 / 0.31 ( 8257) SS BOND : bond 0.00249 / 0.14 ( 6) SS BOND : angle 0.99223 / 0.60 ( 12) hydrogen bonds : bond 0.03321 / 2.23 ( 263) hydrogen bonds : angle 3.92242 / 2.79 ( 717) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.6513 (tpt) cc_final: 0.6305 (tpt) REVERT: A 164 ILE cc_start: 0.8205 (mt) cc_final: 0.7876 (mp) REVERT: A 171 ASN cc_start: 0.9260 (p0) cc_final: 0.9031 (p0) REVERT: A 190 PHE cc_start: 0.9110 (m-10) cc_final: 0.8697 (m-80) REVERT: B 140 ASN cc_start: 0.7806 (m110) cc_final: 0.7366 (m110) REVERT: B 149 MET cc_start: 0.7013 (mpp) cc_final: 0.6467 (mpp) REVERT: B 150 GLU cc_start: 0.7347 (pp20) cc_final: 0.7089 (pp20) REVERT: B 161 TYR cc_start: 0.7494 (m-80) cc_final: 0.7155 (m-80) REVERT: B 174 GLU cc_start: 0.9326 (tp30) cc_final: 0.9016 (mp0) REVERT: B 176 ASN cc_start: 0.8022 (m-40) cc_final: 0.7404 (p0) REVERT: B 184 TYR cc_start: 0.8479 (m-10) cc_final: 0.7925 (m-10) REVERT: B 187 GLN cc_start: 0.8802 (mt0) cc_final: 0.8575 (mt0) REVERT: H 3 GLN cc_start: 0.8263 (mp10) cc_final: 0.7976 (mp10) REVERT: H 47 TRP cc_start: 0.8706 (t60) cc_final: 0.8209 (t60) REVERT: H 73 ASP cc_start: 0.9262 (t0) cc_final: 0.8989 (t0) REVERT: H 81 MET cc_start: 0.6139 (tpt) cc_final: 0.5865 (tpt) REVERT: H 128 PHE cc_start: 0.8413 (m-80) cc_final: 0.8043 (m-80) REVERT: L 4 MET cc_start: 0.5218 (mmm) cc_final: 0.1236 (tpp) REVERT: L 76 PHE cc_start: 0.8002 (m-80) cc_final: 0.7727 (m-80) REVERT: L 91 TYR cc_start: 0.8862 (m-10) cc_final: 0.8332 (m-80) REVERT: L 95 GLN cc_start: 0.8109 (pt0) cc_final: 0.7239 (pm20) REVERT: L 175 ASP cc_start: 0.8732 (m-30) cc_final: 0.8500 (m-30) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0571 time to fit residues: 14.4619 Evaluate side-chains 144 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 43 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.0870 chunk 11 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.0570 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 181 GLN B 120 ASN L 47 GLN L 55 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.144593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.110684 restraints weight = 14735.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.116000 restraints weight = 9668.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.120159 restraints weight = 6939.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.123524 restraints weight = 5268.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.126211 restraints weight = 4143.512| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6091 Z= 0.111 Angle : 0.635 8.398 8269 Z= 0.316 Chirality : 0.044 0.167 945 Planarity : 0.005 0.051 1030 Dihedral : 4.230 15.990 824 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.31), residues: 766 helix: 1.71 (0.33), residues: 247 sheet: 0.28 (0.38), residues: 187 loop : -0.60 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 156 TYR 0.021 0.001 TYR L 191 PHE 0.020 0.002 PHE A 203 TRP 0.035 0.002 TRP L 40 HIS 0.004 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6085) covalent geometry : angle 0.63496 / 0.32 ( 8257) SS BOND : bond 0.00220 / 0.11 ( 6) SS BOND : angle 0.86582 / 0.47 ( 12) hydrogen bonds : bond 0.03381 / 2.23 ( 263) hydrogen bonds : angle 3.92577 / 2.79 ( 717) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8227 (mt) cc_final: 0.7903 (mp) REVERT: A 171 ASN cc_start: 0.9277 (p0) cc_final: 0.9074 (p0) REVERT: A 190 PHE cc_start: 0.9114 (m-10) cc_final: 0.8704 (m-80) REVERT: B 140 ASN cc_start: 0.7764 (m110) cc_final: 0.7280 (m110) REVERT: B 149 MET cc_start: 0.6942 (mpp) cc_final: 0.6449 (mpp) REVERT: B 150 GLU cc_start: 0.7339 (pp20) cc_final: 0.6881 (pp20) REVERT: B 168 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7831 (mm-30) REVERT: B 174 GLU cc_start: 0.9421 (tp30) cc_final: 0.9016 (mp0) REVERT: B 176 ASN cc_start: 0.8035 (m-40) cc_final: 0.7367 (p0) REVERT: B 184 TYR cc_start: 0.8469 (m-10) cc_final: 0.8072 (m-10) REVERT: B 211 ILE cc_start: 0.7543 (mm) cc_final: 0.7259 (mm) REVERT: H 3 GLN cc_start: 0.8316 (mp10) cc_final: 0.8006 (mp10) REVERT: H 47 TRP cc_start: 0.8651 (t60) cc_final: 0.8176 (t60) REVERT: H 73 ASP cc_start: 0.9211 (t0) cc_final: 0.8940 (t0) REVERT: H 81 MET cc_start: 0.6327 (tpt) cc_final: 0.6018 (tpt) REVERT: H 99 ASN cc_start: 0.8749 (t0) cc_final: 0.8422 (p0) REVERT: H 100 VAL cc_start: 0.8855 (t) cc_final: 0.8437 (t) REVERT: H 128 PHE cc_start: 0.8441 (m-80) cc_final: 0.8072 (m-80) REVERT: L 4 MET cc_start: 0.5137 (mmm) cc_final: 0.1314 (tpp) REVERT: L 55 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8459 (mm-40) REVERT: L 76 PHE cc_start: 0.8116 (m-80) cc_final: 0.7769 (m-80) REVERT: L 91 TYR cc_start: 0.8853 (m-10) cc_final: 0.8322 (m-80) REVERT: L 95 GLN cc_start: 0.8312 (pt0) cc_final: 0.7613 (pp30) REVERT: L 175 ASP cc_start: 0.8769 (m-30) cc_final: 0.8543 (m-30) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0532 time to fit residues: 14.2526 Evaluate side-chains 144 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 0.0030 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN B 120 ASN L 47 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.141330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107276 restraints weight = 14913.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.112491 restraints weight = 9852.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.116670 restraints weight = 7106.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.119849 restraints weight = 5410.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.122443 restraints weight = 4284.433| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6091 Z= 0.114 Angle : 0.646 8.683 8269 Z= 0.320 Chirality : 0.044 0.171 945 Planarity : 0.005 0.051 1030 Dihedral : 4.229 16.989 824 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.31), residues: 766 helix: 1.52 (0.33), residues: 253 sheet: 0.29 (0.38), residues: 187 loop : -0.62 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 156 TYR 0.013 0.001 TYR A 182 PHE 0.019 0.002 PHE A 203 TRP 0.030 0.002 TRP L 40 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 6085) covalent geometry : angle 0.64337 / 0.32 ( 8257) SS BOND : bond 0.00245 / 0.12 ( 6) SS BOND : angle 1.62264 / 1.46 ( 12) hydrogen bonds : bond 0.03341 / 2.25 ( 263) hydrogen bonds : angle 3.97562 / 2.82 ( 717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1246.06 seconds wall clock time: 22 minutes 16.84 seconds (1336.84 seconds total)