Starting phenix.real_space_refine on Tue Feb 3 20:13:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwe_62608/02_2026/9kwe_62608.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwe_62608/02_2026/9kwe_62608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kwe_62608/02_2026/9kwe_62608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwe_62608/02_2026/9kwe_62608.map" model { file = "/net/cci-nas-00/data/ceres_data/9kwe_62608/02_2026/9kwe_62608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwe_62608/02_2026/9kwe_62608.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 30 5.16 5 C 4127 2.51 5 N 1107 2.21 5 O 1293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6557 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1597 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain: "F" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1596 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1710 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "L" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Time building chain proxies: 1.57, per 1000 atoms: 0.24 Number of scatterers: 6557 At special positions: 0 Unit cell: (65.22, 155.441, 115.222, 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 30 16.00 O 1293 8.00 N 1107 7.00 C 4127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 126 " distance=1.96 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 220 " distance=1.99 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 126 " distance=2.07 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=1.98 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.00 Simple disulfide: pdb=" SG CYS H 225 " - pdb=" SG CYS L 214 " distance=2.18 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.22 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.06 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: 0.53 Conformation dependent library (CDL) restraints added in 266.1 milliseconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 18 sheets defined 3.9% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 104 through 107 removed outlier: 3.897A pdb=" N GLY F 107 " --> pdb=" O ILE F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 104 through 107' Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.019A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.777A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'L' and resid 121 through 127 Processing sheet with id=AA1, first strand: chain 'E' and resid 33 through 34 removed outlier: 3.657A pdb=" N ALA E 110 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.218A pdb=" N VAL E 75 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER E 69 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.218A pdb=" N VAL E 75 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER E 69 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 189 through 191 removed outlier: 6.474A pdb=" N HIS E 163 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU E 150 " --> pdb=" O THR F 232 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 234 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F 235 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.773A pdb=" N TRP E 179 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 10.202A pdb=" N LEU F 150 " --> pdb=" O GLU E 230 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR E 232 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N VAL F 152 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER E 234 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL F 154 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER E 236 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA F 203 " --> pdb=" O VAL F 194 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL F 194 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA F 205 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL F 190 " --> pdb=" O SER F 207 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 32 through 34 removed outlier: 4.293A pdb=" N SER F 32 " --> pdb=" O PHE F 55 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE F 55 " --> pdb=" O SER F 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 42 through 43 removed outlier: 6.519A pdb=" N ALA F 42 " --> pdb=" O ALA F 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 48 through 49 removed outlier: 7.728A pdb=" N LYS F 108 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP F 102 " --> pdb=" O LYS F 108 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA F 110 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.623A pdb=" N LYS F 66 " --> pdb=" O TYR F 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.658A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.055A pdb=" N GLU H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU H 46 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.898A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA H 145 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 190 " --> pdb=" O HIS H 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.898A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 162 through 163 Processing sheet with id=AB6, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.559A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.653A pdb=" N LYS L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN L 37 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.705A pdb=" N ASN L 137 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 153 through 155 removed outlier: 3.799A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 483 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: 0.89 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 1593 1.33 - 1.47: 2048 1.47 - 1.62: 3017 1.62 - 1.77: 7 1.77 - 1.91: 35 Bond restraints: 6700 Sorted by residual: bond pdb=" CD2 HIS E 163 " pdb=" NE2 HIS E 163 " ideal model delta sigma weight residual 1.374 1.448 -0.074 1.10e-02 8.26e+03 4.58e+01 bond pdb=" CD2 HIS H 209 " pdb=" NE2 HIS H 209 " ideal model delta sigma weight residual 1.374 1.438 -0.064 1.10e-02 8.26e+03 3.43e+01 bond pdb=" CD2 HIS L 189 " pdb=" NE2 HIS L 189 " ideal model delta sigma weight residual 1.374 1.436 -0.062 1.10e-02 8.26e+03 3.16e+01 bond pdb=" CA ARG F 112 " pdb=" C ARG F 112 " ideal model delta sigma weight residual 1.523 1.589 -0.066 1.18e-02 7.18e+03 3.08e+01 bond pdb=" CE1 HIS F 163 " pdb=" NE2 HIS F 163 " ideal model delta sigma weight residual 1.321 1.267 0.054 1.00e-02 1.00e+04 2.92e+01 ... (remaining 6695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 5655 1.74 - 3.48: 2284 3.48 - 5.22: 914 5.22 - 6.97: 205 6.97 - 8.71: 40 Bond angle restraints: 9098 Sorted by residual: angle pdb=" CD2 HIS H 209 " pdb=" NE2 HIS H 209 " pdb=" CE1 HIS H 209 " ideal model delta sigma weight residual 109.00 101.03 7.97 1.00e+00 1.00e+00 6.35e+01 angle pdb=" CD2 HIS L 198 " pdb=" NE2 HIS L 198 " pdb=" CE1 HIS L 198 " ideal model delta sigma weight residual 109.00 102.28 6.72 1.00e+00 1.00e+00 4.52e+01 angle pdb=" CA PRO H 222 " pdb=" C PRO H 222 " pdb=" O PRO H 222 " ideal model delta sigma weight residual 121.31 116.34 4.97 7.40e-01 1.83e+00 4.50e+01 angle pdb=" N GLU L 187 " pdb=" CA GLU L 187 " pdb=" C GLU L 187 " ideal model delta sigma weight residual 112.89 105.06 7.83 1.24e+00 6.50e-01 3.99e+01 angle pdb=" OD1 ASN E 186 " pdb=" CG ASN E 186 " pdb=" ND2 ASN E 186 " ideal model delta sigma weight residual 122.60 116.56 6.04 1.00e+00 1.00e+00 3.65e+01 ... (remaining 9093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3718 17.98 - 35.96: 250 35.96 - 53.95: 36 53.95 - 71.93: 13 71.93 - 89.91: 8 Dihedral angle restraints: 4025 sinusoidal: 1552 harmonic: 2473 Sorted by residual: dihedral pdb=" CB CYS E 166 " pdb=" SG CYS E 166 " pdb=" SG CYS E 220 " pdb=" CB CYS E 220 " ideal model delta sinusoidal sigma weight residual 93.00 36.38 56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CA TYR F 172 " pdb=" C TYR F 172 " pdb=" N PRO F 173 " pdb=" CA PRO F 173 " ideal model delta harmonic sigma weight residual 0.00 -32.35 32.35 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 0.00 30.99 -30.99 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 4022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 654 0.163 - 0.326: 303 0.326 - 0.488: 55 0.488 - 0.651: 4 0.651 - 0.813: 1 Chirality restraints: 1017 Sorted by residual: chirality pdb=" CG LEU E 111 " pdb=" CB LEU E 111 " pdb=" CD1 LEU E 111 " pdb=" CD2 LEU E 111 " both_signs ideal model delta sigma weight residual False -2.59 -1.78 -0.81 2.00e-01 2.50e+01 1.65e+01 chirality pdb=" CB ILE L 2 " pdb=" CA ILE L 2 " pdb=" CG1 ILE L 2 " pdb=" CG2 ILE L 2 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" CG LEU E 34 " pdb=" CB LEU E 34 " pdb=" CD1 LEU E 34 " pdb=" CD2 LEU E 34 " both_signs ideal model delta sigma weight residual False -2.59 -3.14 0.55 2.00e-01 2.50e+01 7.61e+00 ... (remaining 1014 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 179 " 0.097 2.00e-02 2.50e+03 1.09e-01 2.97e+02 pdb=" CG TRP F 179 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 TRP F 179 " -0.139 2.00e-02 2.50e+03 pdb=" CD2 TRP F 179 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP F 179 " -0.093 2.00e-02 2.50e+03 pdb=" CE2 TRP F 179 " -0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP F 179 " -0.089 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 179 " 0.199 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 179 " -0.133 2.00e-02 2.50e+03 pdb=" CH2 TRP F 179 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 35 " 0.027 2.00e-02 2.50e+03 9.09e-02 2.06e+02 pdb=" CG TRP L 35 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP L 35 " -0.153 2.00e-02 2.50e+03 pdb=" CD2 TRP L 35 " 0.132 2.00e-02 2.50e+03 pdb=" NE1 TRP L 35 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP L 35 " 0.098 2.00e-02 2.50e+03 pdb=" CE3 TRP L 35 " 0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 35 " 0.080 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 35 " -0.134 2.00e-02 2.50e+03 pdb=" CH2 TRP L 35 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 32 " -0.064 2.00e-02 2.50e+03 8.41e-02 1.77e+02 pdb=" CG TRP L 32 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP L 32 " 0.157 2.00e-02 2.50e+03 pdb=" CD2 TRP L 32 " -0.031 2.00e-02 2.50e+03 pdb=" NE1 TRP L 32 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TRP L 32 " -0.049 2.00e-02 2.50e+03 pdb=" CE3 TRP L 32 " 0.046 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 32 " -0.112 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 32 " 0.112 2.00e-02 2.50e+03 pdb=" CH2 TRP L 32 " -0.019 2.00e-02 2.50e+03 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 2836 2.93 - 3.43: 5976 3.43 - 3.92: 10029 3.92 - 4.41: 11359 4.41 - 4.90: 19582 Nonbonded interactions: 49782 Sorted by model distance: nonbonded pdb=" O VAL E 190 " pdb=" OG SER E 207 " model vdw 2.443 3.040 nonbonded pdb=" O ALA H 24 " pdb=" OG SER H 77 " model vdw 2.446 3.040 nonbonded pdb=" OG SER E 219 " pdb=" OG SER E 234 " model vdw 2.452 3.040 nonbonded pdb=" OE1 GLN E 178 " pdb=" OD1 ASN E 186 " model vdw 2.456 3.040 nonbonded pdb=" OG1 THR F 189 " pdb=" O SER F 207 " model vdw 2.462 3.040 ... (remaining 49777 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 'E' and (resid 30 through 148 or resid 150 through 152 or resid 154 throu \ gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or \ resid 225 through 241)) selection = (chain 'F' and (resid 30 through 148 or resid 150 through 152 or resid 154 throu \ gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or \ resid 225 through 241)) } 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=0.00 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.760 Find NCS groups from input model: 0.070 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 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 : 0.028 0.188 6708 Z= 1.754 Angle : 2.249 17.561 9114 Z= 1.465 Chirality : 0.172 0.813 1017 Planarity : 0.025 0.109 1174 Dihedral : 13.425 89.910 2425 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.12 % Twisted Proline : 11.36 % Twisted General : 0.12 % 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: -3.76 (0.25), residues: 855 helix: -3.47 (1.34), residues: 7 sheet: -1.92 (0.28), residues: 327 loop : -3.00 (0.23), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.012 ARG E 223 TYR 0.113 0.031 TYR E 124 PHE 0.115 0.040 PHE F 133 TRP 0.199 0.054 TRP F 179 HIS 0.076 0.028 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.02751 ( 6700) covalent geometry : angle 2.21132 ( 9098) SS BOND : bond 0.09459 ( 8) SS BOND : angle 10.00198 ( 16) hydrogen bonds : bond 0.27729 ( 184) hydrogen bonds : angle 12.44867 ( 483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.231 Fit side-chains REVERT: E 117 THR cc_start: 0.8705 (t) cc_final: 0.8323 (m) REVERT: L 28 ASN cc_start: 0.3832 (t0) cc_final: 0.3505 (t0) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0975 time to fit residues: 17.1939 Evaluate side-chains 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.215980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.205730 restraints weight = 9659.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.204880 restraints weight = 12959.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.205175 restraints weight = 12985.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.205750 restraints weight = 9806.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.205767 restraints weight = 9266.923| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6708 Z= 0.162 Angle : 0.695 9.291 9114 Z= 0.362 Chirality : 0.047 0.151 1017 Planarity : 0.006 0.073 1174 Dihedral : 5.929 22.000 926 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.83 % Allowed : 6.91 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.12 % 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: -2.94 (0.27), residues: 855 helix: -0.80 (1.74), residues: 7 sheet: -1.50 (0.27), residues: 344 loop : -2.36 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 73 TYR 0.022 0.002 TYR E 134 PHE 0.013 0.002 PHE H 64 TRP 0.020 0.003 TRP H 36 HIS 0.008 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6700) covalent geometry : angle 0.69339 ( 9098) SS BOND : bond 0.00792 ( 8) SS BOND : angle 1.26534 ( 16) hydrogen bonds : bond 0.04443 ( 184) hydrogen bonds : angle 8.72126 ( 483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: F 223 ARG cc_start: 0.6986 (ttm110) cc_final: 0.6652 (ttm110) REVERT: F 226 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.6941 (pp) REVERT: H 97 SER cc_start: 0.8737 (t) cc_final: 0.8314 (p) REVERT: L 28 ASN cc_start: 0.2982 (t0) cc_final: 0.2677 (t0) REVERT: L 124 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6808 (mm-40) outliers start: 6 outliers final: 5 residues processed: 129 average time/residue: 0.0839 time to fit residues: 14.2694 Evaluate side-chains 114 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 219 SER Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 47 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.218508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.207684 restraints weight = 9491.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.207900 restraints weight = 7889.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.208149 restraints weight = 7071.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.208306 restraints weight = 6185.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.208431 restraints weight = 6111.288| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6708 Z= 0.118 Angle : 0.613 8.296 9114 Z= 0.317 Chirality : 0.045 0.143 1017 Planarity : 0.005 0.061 1174 Dihedral : 5.156 22.894 926 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.52 % Allowed : 9.25 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.12 % 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: -2.48 (0.28), residues: 855 helix: 2.02 (2.10), residues: 7 sheet: -1.19 (0.28), residues: 343 loop : -2.09 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 73 TYR 0.019 0.001 TYR E 134 PHE 0.011 0.001 PHE H 64 TRP 0.026 0.002 TRP H 36 HIS 0.006 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6700) covalent geometry : angle 0.61203 ( 9098) SS BOND : bond 0.00718 ( 8) SS BOND : angle 0.91049 ( 16) hydrogen bonds : bond 0.03321 ( 184) hydrogen bonds : angle 7.59093 ( 483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: F 226 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.6908 (pp) REVERT: L 124 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6881 (mm-40) outliers start: 11 outliers final: 7 residues processed: 117 average time/residue: 0.0805 time to fit residues: 12.4482 Evaluate side-chains 111 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 10 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN E 149 ASN ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 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 = 0.4455 r_free = 0.4455 target = 0.215524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.206324 restraints weight = 9579.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.206054 restraints weight = 12464.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.206620 restraints weight = 11226.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.206966 restraints weight = 8139.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.207220 restraints weight = 7382.055| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6708 Z= 0.141 Angle : 0.616 9.165 9114 Z= 0.320 Chirality : 0.045 0.145 1017 Planarity : 0.005 0.058 1174 Dihedral : 5.076 24.351 926 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.07 % Allowed : 10.08 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.12 % 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: -2.36 (0.29), residues: 855 helix: 1.82 (1.86), residues: 8 sheet: -1.16 (0.28), residues: 352 loop : -1.97 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 73 TYR 0.016 0.002 TYR E 134 PHE 0.022 0.002 PHE H 29 TRP 0.036 0.003 TRP H 36 HIS 0.005 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6700) covalent geometry : angle 0.61493 ( 9098) SS BOND : bond 0.00751 ( 8) SS BOND : angle 1.00442 ( 16) hydrogen bonds : bond 0.03257 ( 184) hydrogen bonds : angle 7.54523 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: E 43 MET cc_start: 0.4718 (ppp) cc_final: 0.4516 (ppp) REVERT: F 223 ARG cc_start: 0.7089 (ttm110) cc_final: 0.6841 (ttm110) REVERT: F 226 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.6962 (pp) REVERT: L 103 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7959 (mmtt) REVERT: L 124 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6844 (mm-40) outliers start: 15 outliers final: 9 residues processed: 122 average time/residue: 0.0773 time to fit residues: 12.5301 Evaluate side-chains 119 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 84 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 67 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.214926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.202212 restraints weight = 9739.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.203305 restraints weight = 7331.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.204404 restraints weight = 5920.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.204885 restraints weight = 4984.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.205304 restraints weight = 4379.358| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6708 Z= 0.142 Angle : 0.611 8.777 9114 Z= 0.319 Chirality : 0.045 0.146 1017 Planarity : 0.005 0.067 1174 Dihedral : 5.044 25.188 926 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.93 % Allowed : 10.77 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.12 % 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: -2.33 (0.29), residues: 855 helix: 1.74 (1.81), residues: 8 sheet: -1.14 (0.28), residues: 353 loop : -1.96 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 73 TYR 0.015 0.002 TYR E 134 PHE 0.011 0.001 PHE E 31 TRP 0.044 0.003 TRP H 36 HIS 0.005 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6700) covalent geometry : angle 0.61034 ( 9098) SS BOND : bond 0.00808 ( 8) SS BOND : angle 0.91719 ( 16) hydrogen bonds : bond 0.03157 ( 184) hydrogen bonds : angle 7.41567 ( 483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: F 226 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.6921 (pp) REVERT: L 103 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7911 (mmtt) REVERT: L 124 GLN cc_start: 0.7407 (mm-40) cc_final: 0.7077 (mm-40) outliers start: 14 outliers final: 8 residues processed: 123 average time/residue: 0.0843 time to fit residues: 13.8038 Evaluate side-chains 119 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 0.0870 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 0.0980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.217487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.207839 restraints weight = 9595.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.207311 restraints weight = 12481.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.207977 restraints weight = 10825.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.208103 restraints weight = 8529.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.208550 restraints weight = 7439.625| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6708 Z= 0.119 Angle : 0.594 8.137 9114 Z= 0.309 Chirality : 0.044 0.144 1017 Planarity : 0.005 0.075 1174 Dihedral : 4.842 26.070 926 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.07 % Allowed : 11.46 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.12 % 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: -2.21 (0.29), residues: 855 helix: 3.01 (2.05), residues: 7 sheet: -1.01 (0.29), residues: 347 loop : -1.91 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 223 TYR 0.016 0.001 TYR E 134 PHE 0.009 0.001 PHE E 31 TRP 0.048 0.002 TRP H 36 HIS 0.004 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6700) covalent geometry : angle 0.59349 ( 9098) SS BOND : bond 0.00752 ( 8) SS BOND : angle 0.79064 ( 16) hydrogen bonds : bond 0.02863 ( 184) hydrogen bonds : angle 7.12457 ( 483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: E 43 MET cc_start: 0.4798 (ppp) cc_final: 0.4597 (ppp) REVERT: E 179 TRP cc_start: 0.5872 (m100) cc_final: 0.5661 (m100) REVERT: F 226 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.6922 (pp) REVERT: H 97 SER cc_start: 0.8788 (t) cc_final: 0.8320 (p) REVERT: L 103 LYS cc_start: 0.8367 (mmtt) cc_final: 0.7894 (mmtt) REVERT: L 124 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6889 (mm-40) outliers start: 15 outliers final: 11 residues processed: 125 average time/residue: 0.0727 time to fit residues: 12.1269 Evaluate side-chains 126 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN L 189 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.217346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.205931 restraints weight = 9421.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.206836 restraints weight = 7728.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.207294 restraints weight = 6459.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.207378 restraints weight = 5644.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.207993 restraints weight = 5378.124| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6708 Z= 0.127 Angle : 0.592 8.061 9114 Z= 0.309 Chirality : 0.045 0.143 1017 Planarity : 0.005 0.070 1174 Dihedral : 4.834 25.757 926 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.21 % Allowed : 12.15 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.12 % 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: -2.18 (0.29), residues: 855 helix: 2.83 (2.00), residues: 7 sheet: -0.99 (0.29), residues: 347 loop : -1.89 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 73 TYR 0.016 0.001 TYR E 134 PHE 0.012 0.001 PHE F 241 TRP 0.048 0.003 TRP H 36 HIS 0.006 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6700) covalent geometry : angle 0.59129 ( 9098) SS BOND : bond 0.01020 ( 8) SS BOND : angle 0.80656 ( 16) hydrogen bonds : bond 0.02920 ( 184) hydrogen bonds : angle 7.05924 ( 483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: E 179 TRP cc_start: 0.5797 (m100) cc_final: 0.5548 (m100) REVERT: L 103 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7969 (mmtt) REVERT: L 124 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7033 (mm-40) outliers start: 16 outliers final: 15 residues processed: 123 average time/residue: 0.0823 time to fit residues: 13.3702 Evaluate side-chains 122 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN E 151 HIS E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.216318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.207433 restraints weight = 9528.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.206780 restraints weight = 12307.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.207251 restraints weight = 10814.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.207358 restraints weight = 8711.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.207463 restraints weight = 7854.736| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6708 Z= 0.136 Angle : 0.611 8.050 9114 Z= 0.320 Chirality : 0.045 0.144 1017 Planarity : 0.005 0.081 1174 Dihedral : 4.902 27.377 926 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.62 % Allowed : 12.85 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.12 % 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: -2.23 (0.29), residues: 855 helix: 2.65 (2.00), residues: 7 sheet: -1.03 (0.28), residues: 347 loop : -1.91 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 73 TYR 0.016 0.002 TYR E 134 PHE 0.027 0.002 PHE H 131 TRP 0.044 0.003 TRP H 36 HIS 0.006 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6700) covalent geometry : angle 0.61064 ( 9098) SS BOND : bond 0.00928 ( 8) SS BOND : angle 0.86287 ( 16) hydrogen bonds : bond 0.02981 ( 184) hydrogen bonds : angle 7.11974 ( 483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: E 179 TRP cc_start: 0.5912 (m100) cc_final: 0.5708 (m100) REVERT: L 103 LYS cc_start: 0.8345 (mmtt) cc_final: 0.8049 (mmtt) outliers start: 19 outliers final: 18 residues processed: 128 average time/residue: 0.0808 time to fit residues: 13.6757 Evaluate side-chains 131 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 219 SER Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN E 174 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN L 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.213486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.204218 restraints weight = 9546.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.203808 restraints weight = 11199.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.203849 restraints weight = 8267.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.204113 restraints weight = 7277.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.204129 restraints weight = 6492.632| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6708 Z= 0.169 Angle : 0.654 8.550 9114 Z= 0.341 Chirality : 0.046 0.147 1017 Planarity : 0.005 0.082 1174 Dihedral : 5.194 29.080 926 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.90 % Allowed : 12.43 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.12 % 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: -2.34 (0.29), residues: 855 helix: 1.69 (1.73), residues: 7 sheet: -1.03 (0.28), residues: 349 loop : -2.04 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 211 TYR 0.017 0.002 TYR E 134 PHE 0.046 0.002 PHE H 29 TRP 0.055 0.003 TRP H 36 HIS 0.007 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6700) covalent geometry : angle 0.65354 ( 9098) SS BOND : bond 0.00926 ( 8) SS BOND : angle 1.02841 ( 16) hydrogen bonds : bond 0.03231 ( 184) hydrogen bonds : angle 7.45120 ( 483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: L 124 GLN cc_start: 0.7410 (mm-40) cc_final: 0.6605 (mm-40) outliers start: 21 outliers final: 18 residues processed: 136 average time/residue: 0.0723 time to fit residues: 13.0457 Evaluate side-chains 137 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 219 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 83 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN E 174 GLN ** F 178 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 = 0.4445 r_free = 0.4445 target = 0.214726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.205468 restraints weight = 9504.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.204182 restraints weight = 10601.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.204725 restraints weight = 8510.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.205216 restraints weight = 7272.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.205216 restraints weight = 6331.853| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6708 Z= 0.148 Angle : 0.638 8.357 9114 Z= 0.332 Chirality : 0.045 0.149 1017 Planarity : 0.005 0.088 1174 Dihedral : 5.121 28.694 926 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.62 % Allowed : 13.40 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.12 % 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: -2.35 (0.28), residues: 855 helix: 1.87 (1.85), residues: 7 sheet: -1.01 (0.29), residues: 336 loop : -2.07 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 73 TYR 0.017 0.002 TYR E 134 PHE 0.019 0.002 PHE H 131 TRP 0.059 0.003 TRP H 36 HIS 0.006 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6700) covalent geometry : angle 0.63799 ( 9098) SS BOND : bond 0.00829 ( 8) SS BOND : angle 0.86691 ( 16) hydrogen bonds : bond 0.03013 ( 184) hydrogen bonds : angle 7.31478 ( 483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: E 179 TRP cc_start: 0.5874 (m100) cc_final: 0.5667 (m100) REVERT: H 97 SER cc_start: 0.8776 (t) cc_final: 0.8371 (p) REVERT: L 28 ASN cc_start: 0.3275 (t0) cc_final: 0.3030 (t0) REVERT: L 124 GLN cc_start: 0.7385 (mm-40) cc_final: 0.6723 (mm-40) outliers start: 19 outliers final: 17 residues processed: 130 average time/residue: 0.0702 time to fit residues: 12.1602 Evaluate side-chains 132 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 219 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 178 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.215557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.206455 restraints weight = 9426.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.206527 restraints weight = 10173.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.206740 restraints weight = 6880.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.206731 restraints weight = 6370.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.206777 restraints weight = 5778.348| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6708 Z= 0.139 Angle : 0.632 8.238 9114 Z= 0.328 Chirality : 0.045 0.147 1017 Planarity : 0.005 0.088 1174 Dihedral : 5.029 27.372 926 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.35 % Allowed : 13.67 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.12 % 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: -2.33 (0.28), residues: 855 helix: 1.87 (1.83), residues: 7 sheet: -0.98 (0.29), residues: 338 loop : -2.06 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 73 TYR 0.017 0.002 TYR E 134 PHE 0.017 0.001 PHE H 131 TRP 0.062 0.003 TRP H 36 HIS 0.004 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6700) covalent geometry : angle 0.63101 ( 9098) SS BOND : bond 0.00811 ( 8) SS BOND : angle 0.89654 ( 16) hydrogen bonds : bond 0.02905 ( 184) hydrogen bonds : angle 7.19359 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1116.25 seconds wall clock time: 20 minutes 3.23 seconds (1203.23 seconds total)