Starting phenix.real_space_refine on Sun Aug 24 08:18:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ok3_70553/08_2025/9ok3_70553.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ok3_70553/08_2025/9ok3_70553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ok3_70553/08_2025/9ok3_70553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ok3_70553/08_2025/9ok3_70553.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ok3_70553/08_2025/9ok3_70553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ok3_70553/08_2025/9ok3_70553.map" } resolution = 3.74 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= 0.048 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: 5 Type Number sf(0) Gaussians S 76 5.16 5 C 5585 2.51 5 N 1521 2.21 5 O 1771 1.98 5 H 8786 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17739 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1022 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "A" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1162 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "C" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2464 Classifications: {'peptide': 157} Link IDs: {'TRANS': 156} Chain breaks: 1 Chain: "F" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4467 Classifications: {'peptide': 287} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain: "G" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4319 Classifications: {'peptide': 276} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 272} Chain breaks: 1 Chain: "H" Number of atoms: 4305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 4305 Classifications: {'peptide': 275} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 271} Chain breaks: 1 Time building chain proxies: 3.11, per 1000 atoms: 0.18 Number of scatterers: 17739 At special positions: 0 Unit cell: (108.504, 87.68, 132.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 O 1771 8.00 N 1521 7.00 C 5585 6.00 H 8786 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 509.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 0 sheets defined 93.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 197 through 259 removed outlier: 3.723A pdb=" N TYR B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 201 through 259 removed outlier: 3.527A pdb=" N LEU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 82 removed outlier: 4.138A pdb=" N LYS C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 202 removed outlier: 4.234A pdb=" N ASN C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS C 162 " --> pdb=" O GLY C 158 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU C 170 " --> pdb=" O ASP C 166 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE C 171 " --> pdb=" O MET C 167 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR C 173 " --> pdb=" O ASN C 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 32 removed outlier: 3.775A pdb=" N GLN F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 55 Processing helix chain 'F' and resid 57 through 75 Processing helix chain 'F' and resid 77 through 93 Processing helix chain 'F' and resid 98 through 114 removed outlier: 3.715A pdb=" N ASN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 135 removed outlier: 3.671A pdb=" N ALA F 120 " --> pdb=" O ARG F 116 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 155 removed outlier: 3.613A pdb=" N ALA F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 173 Processing helix chain 'F' and resid 174 through 176 No H-bonds generated for 'chain 'F' and resid 174 through 176' Processing helix chain 'F' and resid 177 through 194 removed outlier: 4.571A pdb=" N ALA F 181 " --> pdb=" O GLN F 177 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP F 194 " --> pdb=" O THR F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 215 removed outlier: 4.357A pdb=" N LYS F 203 " --> pdb=" O LYS F 199 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP F 204 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE F 206 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS F 215 " --> pdb=" O LEU F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.768A pdb=" N LEU F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F 224 " --> pdb=" O ASN F 220 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 238 through 252 removed outlier: 4.022A pdb=" N LYS F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 270 Processing helix chain 'F' and resid 273 through 285 Processing helix chain 'G' and resid 1 through 23 Processing helix chain 'G' and resid 39 through 56 Processing helix chain 'G' and resid 60 through 75 removed outlier: 3.898A pdb=" N LEU G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 96 removed outlier: 4.478A pdb=" N LYS G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA G 95 " --> pdb=" O ALA G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 115 removed outlier: 3.835A pdb=" N ALA G 100 " --> pdb=" O ASP G 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 101 " --> pdb=" O PRO G 97 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 134 Processing helix chain 'G' and resid 138 through 155 Processing helix chain 'G' and resid 157 through 176 Processing helix chain 'G' and resid 178 through 195 removed outlier: 4.122A pdb=" N ASP G 194 " --> pdb=" O THR G 190 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER G 195 " --> pdb=" O SER G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 200 removed outlier: 4.327A pdb=" N TYR G 200 " --> pdb=" O LEU G 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 197 through 200' Processing helix chain 'G' and resid 201 through 217 removed outlier: 4.173A pdb=" N TYR G 205 " --> pdb=" O SER G 201 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE G 216 " --> pdb=" O CYS G 212 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP G 217 " --> pdb=" O HIS G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 232 removed outlier: 3.527A pdb=" N ALA G 221 " --> pdb=" O ASP G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 237 Processing helix chain 'G' and resid 238 through 252 removed outlier: 3.555A pdb=" N LYS G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 270 removed outlier: 3.722A pdb=" N TYR G 259 " --> pdb=" O ASN G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 286 removed outlier: 3.692A pdb=" N THR G 278 " --> pdb=" O GLN G 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 23 Processing helix chain 'H' and resid 37 through 56 Processing helix chain 'H' and resid 57 through 75 Processing helix chain 'H' and resid 78 through 93 Processing helix chain 'H' and resid 96 through 114 removed outlier: 3.704A pdb=" N ALA H 100 " --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 134 removed outlier: 3.534A pdb=" N ALA H 120 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 155 removed outlier: 4.126A pdb=" N ALA H 141 " --> pdb=" O ASP H 137 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 176 Processing helix chain 'H' and resid 177 through 195 removed outlier: 3.715A pdb=" N ALA H 181 " --> pdb=" O GLN H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 201 through 217 removed outlier: 3.956A pdb=" N TYR H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE H 216 " --> pdb=" O CYS H 212 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP H 217 " --> pdb=" O HIS H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 232 removed outlier: 3.703A pdb=" N LYS H 222 " --> pdb=" O MET H 218 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU H 223 " --> pdb=" O LEU H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 237 Processing helix chain 'H' and resid 238 through 252 removed outlier: 3.656A pdb=" N LYS H 242 " --> pdb=" O SER H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 270 removed outlier: 3.514A pdb=" N THR H 260 " --> pdb=" O VAL H 256 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE H 269 " --> pdb=" O GLU H 265 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER H 270 " --> pdb=" O TYR H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 286 removed outlier: 3.786A pdb=" N THR H 286 " --> pdb=" O ARG H 282 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2328 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: 3.88 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8762 1.03 - 1.23: 29 1.23 - 1.42: 3779 1.42 - 1.62: 5165 1.62 - 1.81: 128 Bond restraints: 17863 Sorted by residual: bond pdb=" C HIS G 123 " pdb=" N HIS G 124 " ideal model delta sigma weight residual 1.335 1.466 -0.131 1.31e-02 5.83e+03 9.97e+01 bond pdb=" CA SER A 200 " pdb=" CB SER A 200 " ideal model delta sigma weight residual 1.534 1.461 0.073 1.58e-02 4.01e+03 2.12e+01 bond pdb=" CA ALA G 121 " pdb=" CB ALA G 121 " ideal model delta sigma weight residual 1.529 1.459 0.070 1.55e-02 4.16e+03 2.03e+01 bond pdb=" C ASP F 87 " pdb=" N ALA F 88 " ideal model delta sigma weight residual 1.335 1.394 -0.059 1.31e-02 5.83e+03 2.02e+01 bond pdb=" C LYS G 122 " pdb=" O LYS G 122 " ideal model delta sigma weight residual 1.237 1.277 -0.040 1.16e-02 7.43e+03 1.20e+01 ... (remaining 17858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 31835 1.82 - 3.64: 338 3.64 - 5.45: 30 5.45 - 7.27: 4 7.27 - 9.09: 5 Bond angle restraints: 32212 Sorted by residual: angle pdb=" O ARG A 198 " pdb=" C ARG A 198 " pdb=" N HIS A 199 " ideal model delta sigma weight residual 122.09 116.99 5.10 1.04e+00 9.25e-01 2.40e+01 angle pdb=" C HIS G 123 " pdb=" CA HIS G 123 " pdb=" CB HIS G 123 " ideal model delta sigma weight residual 110.79 118.77 -7.98 1.66e+00 3.63e-01 2.31e+01 angle pdb=" CA ARG A 198 " pdb=" C ARG A 198 " pdb=" N HIS A 199 " ideal model delta sigma weight residual 116.97 122.22 -5.25 1.20e+00 6.94e-01 1.92e+01 angle pdb=" CA GLU A 206 " pdb=" C GLU A 206 " pdb=" O GLU A 206 " ideal model delta sigma weight residual 120.42 116.00 4.42 1.06e+00 8.90e-01 1.74e+01 angle pdb=" N GLU A 201 " pdb=" CA GLU A 201 " pdb=" C GLU A 201 " ideal model delta sigma weight residual 112.90 107.54 5.36 1.31e+00 5.83e-01 1.67e+01 ... (remaining 32207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 7299 17.67 - 35.35: 752 35.35 - 53.02: 226 53.02 - 70.70: 63 70.70 - 88.37: 16 Dihedral angle restraints: 8356 sinusoidal: 4513 harmonic: 3843 Sorted by residual: dihedral pdb=" CA GLN F 177 " pdb=" C GLN F 177 " pdb=" N TYR F 178 " pdb=" CA TYR F 178 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LEU A 192 " pdb=" C LEU A 192 " pdb=" N SER A 193 " pdb=" CA SER A 193 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP G 80 " pdb=" CB ASP G 80 " pdb=" CG ASP G 80 " pdb=" OD1 ASP G 80 " ideal model delta sinusoidal sigma weight residual -30.00 -88.17 58.17 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 8353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 961 0.026 - 0.052: 228 0.052 - 0.078: 101 0.078 - 0.104: 35 0.104 - 0.131: 8 Chirality restraints: 1333 Sorted by residual: chirality pdb=" CB THR H 112 " pdb=" CA THR H 112 " pdb=" OG1 THR H 112 " pdb=" CG2 THR H 112 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CB THR A 197 " pdb=" CA THR A 197 " pdb=" OG1 THR A 197 " pdb=" CG2 THR A 197 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE C 134 " pdb=" N ILE C 134 " pdb=" C ILE C 134 " pdb=" CB ILE C 134 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 1330 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 200 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C SER A 200 " 0.032 2.00e-02 2.50e+03 pdb=" O SER A 200 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU A 201 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 199 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C HIS A 199 " -0.030 2.00e-02 2.50e+03 pdb=" O HIS A 199 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 200 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 273 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C ASP G 273 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP G 273 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN G 274 " 0.010 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1349 2.21 - 2.81: 35886 2.81 - 3.40: 48284 3.40 - 4.00: 55725 4.00 - 4.60: 89288 Nonbonded interactions: 230532 Sorted by model distance: nonbonded pdb=" OE1 GLU F 99 " pdb=" H GLU F 99 " model vdw 1.609 2.450 nonbonded pdb=" OE1 GLU H 139 " pdb=" H GLU H 139 " model vdw 1.613 2.450 nonbonded pdb=" O VAL F 21 " pdb=" HG SER F 24 " model vdw 1.620 2.450 nonbonded pdb=" OD1 ASP F 273 " pdb=" H GLN F 274 " model vdw 1.633 2.450 nonbonded pdb=" O GLU H 265 " pdb=" HG SER H 268 " model vdw 1.633 2.450 ... (remaining 230527 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' and ((resid 197 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 198 through 259)) selection = chain 'B' } ncs_group { reference = (chain 'F' and (resid 0 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG ) \ ) or (resid 38 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG13 or name \ HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13)) or resi \ d 39 through 286)) selection = (chain 'G' and (resid 0 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG ) \ ) or resid 38 through 286)) selection = (chain 'H' and (resid 0 through 36 or (resid 38 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB \ or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or \ name HD12 or name HD13)) or resid 39 through 286)) } 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: 1.470 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: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.280 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 0.131 9077 Z= 0.235 Angle : 0.607 9.090 12176 Z= 0.369 Chirality : 0.031 0.131 1333 Planarity : 0.003 0.032 1582 Dihedral : 18.045 88.371 3434 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.16 % Favored : 97.75 % Rotamer: Outliers : 0.74 % Allowed : 25.32 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.24), residues: 1112 helix: 2.08 (0.16), residues: 979 sheet: None (None), residues: 0 loop : -2.13 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.019 0.001 TYR G 131 PHE 0.017 0.001 PHE H 65 TRP 0.012 0.002 TRP F 275 HIS 0.007 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9077) covalent geometry : angle 0.60707 (12176) hydrogen bonds : bond 0.12163 ( 782) hydrogen bonds : angle 5.37825 ( 2328) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 189 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 MET cc_start: 0.7706 (ptm) cc_final: 0.7312 (ppp) REVERT: B 248 VAL cc_start: 0.7794 (p) cc_final: 0.7505 (p) outliers start: 7 outliers final: 5 residues processed: 194 average time/residue: 0.2435 time to fit residues: 63.0722 Evaluate side-chains 179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 174 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 51 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN A 199 HIS C 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.140873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108943 restraints weight = 49168.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108741 restraints weight = 23622.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109476 restraints weight = 19971.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110115 restraints weight = 15704.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110187 restraints weight = 15182.336| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9077 Z= 0.189 Angle : 0.530 6.517 12176 Z= 0.309 Chirality : 0.030 0.127 1333 Planarity : 0.003 0.030 1582 Dihedral : 5.019 55.415 1225 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.58 % Allowed : 25.32 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.24), residues: 1112 helix: 2.37 (0.15), residues: 987 sheet: None (None), residues: 0 loop : -1.82 (0.61), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 198 TYR 0.018 0.001 TYR A 243 PHE 0.014 0.002 PHE H 65 TRP 0.012 0.002 TRP F 275 HIS 0.005 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9077) covalent geometry : angle 0.53026 (12176) hydrogen bonds : bond 0.07341 ( 782) hydrogen bonds : angle 4.53762 ( 2328) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 155 GLU cc_start: 0.8350 (tp30) cc_final: 0.7700 (tp30) REVERT: F 213 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.6952 (t-170) REVERT: G 51 MET cc_start: 0.8494 (ptp) cc_final: 0.8288 (ptp) REVERT: H 279 MET cc_start: 0.8516 (tpp) cc_final: 0.8242 (tpp) outliers start: 15 outliers final: 12 residues processed: 194 average time/residue: 0.2319 time to fit residues: 60.0889 Evaluate side-chains 190 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 213 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 237 ASP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 102 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.143816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109540 restraints weight = 48116.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112183 restraints weight = 22833.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113208 restraints weight = 15952.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113306 restraints weight = 13289.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115111 restraints weight = 12563.409| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9077 Z= 0.151 Angle : 0.477 6.445 12176 Z= 0.276 Chirality : 0.029 0.125 1333 Planarity : 0.003 0.055 1582 Dihedral : 4.860 55.062 1225 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.22 % Allowed : 24.05 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.36 (0.24), residues: 1112 helix: 2.67 (0.15), residues: 990 sheet: None (None), residues: 0 loop : -1.97 (0.62), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 19 TYR 0.015 0.001 TYR A 243 PHE 0.012 0.001 PHE H 65 TRP 0.010 0.001 TRP F 275 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9077) covalent geometry : angle 0.47741 (12176) hydrogen bonds : bond 0.06628 ( 782) hydrogen bonds : angle 4.16336 ( 2328) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 VAL cc_start: 0.7661 (p) cc_final: 0.7368 (p) REVERT: C 177 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8321 (mm-40) REVERT: F 155 GLU cc_start: 0.8222 (tp30) cc_final: 0.7705 (tp30) REVERT: F 213 HIS cc_start: 0.8082 (OUTLIER) cc_final: 0.7054 (t-170) REVERT: H 279 MET cc_start: 0.8661 (tpp) cc_final: 0.8009 (mpp) outliers start: 21 outliers final: 17 residues processed: 208 average time/residue: 0.2216 time to fit residues: 62.2457 Evaluate side-chains 195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 72 HIS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 213 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 102 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.142986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110123 restraints weight = 48342.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113704 restraints weight = 26296.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114714 restraints weight = 15124.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114817 restraints weight = 13119.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115095 restraints weight = 11587.529| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9077 Z= 0.157 Angle : 0.488 6.995 12176 Z= 0.282 Chirality : 0.030 0.153 1333 Planarity : 0.003 0.046 1582 Dihedral : 4.522 47.899 1222 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.53 % Allowed : 24.47 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.37 (0.24), residues: 1112 helix: 2.69 (0.15), residues: 990 sheet: None (None), residues: 0 loop : -2.04 (0.61), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 19 TYR 0.015 0.001 TYR A 243 PHE 0.012 0.001 PHE H 65 TRP 0.009 0.001 TRP F 275 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9077) covalent geometry : angle 0.48835 (12176) hydrogen bonds : bond 0.06552 ( 782) hydrogen bonds : angle 4.12075 ( 2328) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 THR cc_start: 0.8143 (m) cc_final: 0.7816 (p) REVERT: C 72 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8121 (ttmm) REVERT: C 177 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8348 (mm-40) REVERT: F 155 GLU cc_start: 0.8275 (tp30) cc_final: 0.7770 (tp30) REVERT: F 213 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7270 (t-170) REVERT: H 6 LYS cc_start: 0.7695 (mmmt) cc_final: 0.7485 (mtpt) REVERT: H 279 MET cc_start: 0.8740 (tpp) cc_final: 0.7932 (mpp) outliers start: 24 outliers final: 19 residues processed: 205 average time/residue: 0.2010 time to fit residues: 55.9733 Evaluate side-chains 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 72 HIS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 213 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 201 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 109 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.141547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.108876 restraints weight = 47771.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110162 restraints weight = 21505.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111959 restraints weight = 17035.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112332 restraints weight = 13344.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112521 restraints weight = 11699.467| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9077 Z= 0.174 Angle : 0.503 7.286 12176 Z= 0.291 Chirality : 0.030 0.165 1333 Planarity : 0.003 0.052 1582 Dihedral : 4.636 47.483 1222 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.74 % Allowed : 25.53 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.23 (0.24), residues: 1112 helix: 2.61 (0.15), residues: 992 sheet: None (None), residues: 0 loop : -2.32 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 19 TYR 0.017 0.001 TYR A 243 PHE 0.012 0.001 PHE H 65 TRP 0.009 0.001 TRP F 275 HIS 0.005 0.001 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9077) covalent geometry : angle 0.50257 (12176) hydrogen bonds : bond 0.06727 ( 782) hydrogen bonds : angle 4.17961 ( 2328) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 THR cc_start: 0.8187 (m) cc_final: 0.7922 (p) REVERT: F 9 GLU cc_start: 0.8236 (pp20) cc_final: 0.7975 (pp20) REVERT: F 155 GLU cc_start: 0.8349 (tp30) cc_final: 0.7878 (tp30) REVERT: F 213 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7332 (t-170) REVERT: F 226 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: G 131 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7080 (t80) REVERT: H 6 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7507 (mtpt) REVERT: H 279 MET cc_start: 0.8865 (tpp) cc_final: 0.8053 (mpp) outliers start: 26 outliers final: 23 residues processed: 205 average time/residue: 0.2076 time to fit residues: 58.4149 Evaluate side-chains 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 72 HIS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 213 HIS Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 237 ASP Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 201 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.143536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110265 restraints weight = 47636.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111844 restraints weight = 22994.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112905 restraints weight = 16351.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113444 restraints weight = 13554.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.113625 restraints weight = 11998.699| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9077 Z= 0.142 Angle : 0.480 7.502 12176 Z= 0.273 Chirality : 0.029 0.158 1333 Planarity : 0.003 0.052 1582 Dihedral : 4.489 48.262 1220 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.64 % Allowed : 25.53 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.47 (0.24), residues: 1112 helix: 2.77 (0.15), residues: 992 sheet: None (None), residues: 0 loop : -2.26 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 19 TYR 0.015 0.001 TYR A 243 PHE 0.012 0.001 PHE A 216 TRP 0.009 0.001 TRP F 275 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9077) covalent geometry : angle 0.47966 (12176) hydrogen bonds : bond 0.06197 ( 782) hydrogen bonds : angle 3.98453 ( 2328) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 THR cc_start: 0.8278 (m) cc_final: 0.8038 (p) REVERT: F 155 GLU cc_start: 0.8325 (tp30) cc_final: 0.7908 (tp30) REVERT: F 213 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7168 (t-170) REVERT: G 131 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7112 (t80) REVERT: H 279 MET cc_start: 0.8896 (tpp) cc_final: 0.8009 (mpp) outliers start: 25 outliers final: 20 residues processed: 208 average time/residue: 0.2079 time to fit residues: 59.1347 Evaluate side-chains 202 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 72 HIS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 213 HIS Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 201 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.142898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110243 restraints weight = 49322.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111025 restraints weight = 22853.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111350 restraints weight = 19033.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112240 restraints weight = 15465.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112212 restraints weight = 14076.967| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9077 Z= 0.145 Angle : 0.493 7.822 12176 Z= 0.279 Chirality : 0.029 0.124 1333 Planarity : 0.003 0.052 1582 Dihedral : 4.494 51.085 1220 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.85 % Allowed : 25.63 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.60 (0.24), residues: 1112 helix: 2.86 (0.15), residues: 992 sheet: None (None), residues: 0 loop : -2.28 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 8 TYR 0.017 0.001 TYR A 243 PHE 0.012 0.001 PHE A 216 TRP 0.009 0.001 TRP F 275 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9077) covalent geometry : angle 0.49254 (12176) hydrogen bonds : bond 0.06072 ( 782) hydrogen bonds : angle 3.94129 ( 2328) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 238 GLU cc_start: 0.8101 (tp30) cc_final: 0.7840 (tp30) REVERT: B 251 THR cc_start: 0.8226 (m) cc_final: 0.7987 (p) REVERT: A 244 VAL cc_start: 0.8906 (t) cc_final: 0.8625 (p) REVERT: F 155 GLU cc_start: 0.8380 (tp30) cc_final: 0.7947 (tp30) REVERT: F 213 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7192 (t-170) REVERT: F 226 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: G 131 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7118 (t80) REVERT: H 279 MET cc_start: 0.8941 (tpp) cc_final: 0.8004 (mpp) outliers start: 27 outliers final: 22 residues processed: 208 average time/residue: 0.2201 time to fit residues: 61.2276 Evaluate side-chains 201 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain F residue 72 HIS Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 213 HIS Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 201 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.141940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109689 restraints weight = 48349.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109939 restraints weight = 22896.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110206 restraints weight = 18794.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110990 restraints weight = 16047.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111121 restraints weight = 14636.728| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9077 Z= 0.155 Angle : 0.502 8.055 12176 Z= 0.285 Chirality : 0.029 0.124 1333 Planarity : 0.003 0.062 1582 Dihedral : 4.535 54.765 1220 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.16 % Allowed : 25.63 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.53 (0.24), residues: 1112 helix: 2.82 (0.15), residues: 992 sheet: None (None), residues: 0 loop : -2.38 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 19 TYR 0.012 0.001 TYR A 243 PHE 0.015 0.001 PHE H 214 TRP 0.008 0.001 TRP F 275 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9077) covalent geometry : angle 0.50207 (12176) hydrogen bonds : bond 0.06173 ( 782) hydrogen bonds : angle 3.99087 ( 2328) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 238 GLU cc_start: 0.8188 (tp30) cc_final: 0.7951 (tp30) REVERT: B 251 THR cc_start: 0.8142 (m) cc_final: 0.7937 (p) REVERT: F 155 GLU cc_start: 0.8420 (tp30) cc_final: 0.7994 (tp30) REVERT: F 213 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7303 (t-170) REVERT: F 226 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7742 (mp10) REVERT: G 131 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7129 (t80) REVERT: H 279 MET cc_start: 0.8956 (tpp) cc_final: 0.8021 (mpp) outliers start: 30 outliers final: 25 residues processed: 208 average time/residue: 0.2211 time to fit residues: 61.7382 Evaluate side-chains 206 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain F residue 72 HIS Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 213 HIS Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 212 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.142555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108882 restraints weight = 49318.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112359 restraints weight = 25675.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112874 restraints weight = 15983.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113410 restraints weight = 14226.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113384 restraints weight = 13343.945| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9077 Z= 0.148 Angle : 0.502 8.246 12176 Z= 0.284 Chirality : 0.029 0.128 1333 Planarity : 0.003 0.055 1582 Dihedral : 4.545 57.859 1220 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.95 % Allowed : 25.63 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.60 (0.24), residues: 1112 helix: 2.88 (0.15), residues: 991 sheet: None (None), residues: 0 loop : -2.43 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 19 TYR 0.012 0.001 TYR A 243 PHE 0.015 0.001 PHE H 214 TRP 0.008 0.001 TRP F 275 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9077) covalent geometry : angle 0.50166 (12176) hydrogen bonds : bond 0.06011 ( 782) hydrogen bonds : angle 3.93836 ( 2328) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 THR cc_start: 0.8070 (m) cc_final: 0.7850 (p) REVERT: F 155 GLU cc_start: 0.8301 (tp30) cc_final: 0.7967 (tp30) REVERT: F 213 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7217 (t-170) REVERT: F 226 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: G 131 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7179 (t80) REVERT: G 285 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8043 (tptt) REVERT: H 279 MET cc_start: 0.8907 (tpp) cc_final: 0.7990 (mpp) outliers start: 28 outliers final: 24 residues processed: 204 average time/residue: 0.2261 time to fit residues: 61.6684 Evaluate side-chains 200 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain F residue 72 HIS Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 213 HIS Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN B 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.144609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112700 restraints weight = 48532.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112003 restraints weight = 24862.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113538 restraints weight = 18509.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114070 restraints weight = 14801.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114133 restraints weight = 14065.603| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9077 Z= 0.130 Angle : 0.499 8.229 12176 Z= 0.277 Chirality : 0.029 0.128 1333 Planarity : 0.003 0.062 1582 Dihedral : 4.469 59.374 1220 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.53 % Allowed : 26.48 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.87 (0.24), residues: 1112 helix: 3.05 (0.15), residues: 991 sheet: None (None), residues: 0 loop : -2.25 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 19 TYR 0.011 0.001 TYR A 243 PHE 0.013 0.001 PHE H 214 TRP 0.009 0.001 TRP F 275 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9077) covalent geometry : angle 0.49863 (12176) hydrogen bonds : bond 0.05448 ( 782) hydrogen bonds : angle 3.75322 ( 2328) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 238 GLU cc_start: 0.8166 (tp30) cc_final: 0.7965 (tp30) REVERT: B 251 THR cc_start: 0.8099 (m) cc_final: 0.7891 (p) REVERT: A 244 VAL cc_start: 0.8757 (t) cc_final: 0.8512 (p) REVERT: F 155 GLU cc_start: 0.8291 (tp30) cc_final: 0.8033 (tp30) REVERT: F 204 ASP cc_start: 0.8529 (t0) cc_final: 0.8134 (m-30) REVERT: F 213 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7176 (t-170) REVERT: F 226 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: G 131 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7026 (t80) outliers start: 24 outliers final: 19 residues processed: 203 average time/residue: 0.2410 time to fit residues: 65.8399 Evaluate side-chains 197 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain F residue 72 HIS Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 213 HIS Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 201 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN B 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.143179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109219 restraints weight = 48756.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111055 restraints weight = 22363.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111589 restraints weight = 17573.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112097 restraints weight = 16097.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112345 restraints weight = 14453.873| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9077 Z= 0.149 Angle : 0.524 8.579 12176 Z= 0.292 Chirality : 0.029 0.125 1333 Planarity : 0.003 0.064 1582 Dihedral : 4.261 57.235 1217 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.64 % Allowed : 26.79 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.24), residues: 1112 helix: 3.01 (0.15), residues: 992 sheet: None (None), residues: 0 loop : -2.35 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 19 TYR 0.011 0.001 TYR H 259 PHE 0.016 0.001 PHE H 214 TRP 0.008 0.001 TRP F 275 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9077) covalent geometry : angle 0.52396 (12176) hydrogen bonds : bond 0.05768 ( 782) hydrogen bonds : angle 3.85412 ( 2328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2819.89 seconds wall clock time: 48 minutes 53.39 seconds (2933.39 seconds total)