Starting phenix.real_space_refine on Fri Aug 22 19:26:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umd_42376/08_2025/8umd_42376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umd_42376/08_2025/8umd_42376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8umd_42376/08_2025/8umd_42376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umd_42376/08_2025/8umd_42376.map" model { file = "/net/cci-nas-00/data/ceres_data/8umd_42376/08_2025/8umd_42376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umd_42376/08_2025/8umd_42376.cif" } resolution = 3.6 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= 0.006 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4528 2.51 5 N 1287 2.21 5 O 1359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s 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: 7201 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 393 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2583 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 324} Chain: "C" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2348 Classifications: {'peptide': 290} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 267} Chain: "D" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 625 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "E" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 625 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 627 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Time building chain proxies: 1.95, per 1000 atoms: 0.27 Number of scatterers: 7201 At special positions: 0 Unit cell: (106.496, 109.824, 168.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1359 8.00 N 1287 7.00 C 4528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 376.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 51.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 514 through 543 Processing helix chain 'A' and resid 543 through 558 Processing helix chain 'B' and resid 5 through 18 removed outlier: 3.832A pdb=" N GLY B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 48 through 67 Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.574A pdb=" N ARG B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLU B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N GLU B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG B 101 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.667A pdb=" N THR B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.635A pdb=" N HIS B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 168 through 183 Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 207 through 222 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.517A pdb=" N LEU B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 242 through 252 removed outlier: 4.062A pdb=" N SER B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.647A pdb=" N LYS B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 297 through 318 removed outlier: 3.510A pdb=" N THR B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 74 Processing helix chain 'C' and resid 89 through 95 removed outlier: 3.619A pdb=" N ASN C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 131 Processing helix chain 'C' and resid 147 through 171 removed outlier: 4.016A pdb=" N ALA C 171 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 227 through 233 removed outlier: 3.854A pdb=" N ASN C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'D' and resid 74 through 81 Processing helix chain 'D' and resid 127 through 134 Processing helix chain 'E' and resid 75 through 81 Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.630A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 130 through 135' Processing helix chain 'F' and resid 75 through 81 Processing helix chain 'F' and resid 127 through 136 Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36 removed outlier: 5.517A pdb=" N LEU E 105 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 101 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 107 " --> pdb=" O ILE E 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP E 98 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 86 through 92 removed outlier: 4.973A pdb=" N TYR F 118 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLN F 108 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE F 125 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ILE F 106 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE F 99 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN F 108 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU F 97 " --> pdb=" O GLN F 108 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL F 62 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG E 72 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU F 64 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG E 70 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL F 66 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL E 66 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP E 98 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 107 " --> pdb=" O ILE E 99 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 101 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU E 105 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 81 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 81 removed outlier: 4.011A pdb=" N ARG C 181 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS C 106 " --> pdb=" O TYR C 179 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR C 179 " --> pdb=" O HIS C 106 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS C 108 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL C 177 " --> pdb=" O LYS C 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 283 through 284 removed outlier: 3.509A pdb=" N VAL D 120 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN D 108 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE D 125 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ILE D 106 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU D 105 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE D 101 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 107 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 98 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL D 62 " --> pdb=" O PRO C 269 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU D 64 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP C 267 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL D 66 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA C 263 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG D 70 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU C 261 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE C 293 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL C 296 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL C 301 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU C 320 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR C 303 " --> pdb=" O GLU C 318 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR C 313 " --> pdb=" O LEU D 89 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2499 1.34 - 1.46: 1323 1.46 - 1.58: 3415 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7290 Sorted by residual: bond pdb=" N THR B 103 " pdb=" CA THR B 103 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.32e+00 bond pdb=" CB ASP E 59 " pdb=" CG ASP E 59 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.89e+00 bond pdb=" CA ASP D 116 " pdb=" CB ASP D 116 " ideal model delta sigma weight residual 1.530 1.553 -0.022 1.69e-02 3.50e+03 1.76e+00 bond pdb=" CA MET E 58 " pdb=" CB MET E 58 " ideal model delta sigma weight residual 1.537 1.560 -0.023 1.85e-02 2.92e+03 1.54e+00 bond pdb=" CB ASP D 116 " pdb=" CG ASP D 116 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.49e+00 ... (remaining 7285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 9691 2.44 - 4.89: 148 4.89 - 7.33: 19 7.33 - 9.77: 5 9.77 - 12.21: 2 Bond angle restraints: 9865 Sorted by residual: angle pdb=" CA MET E 58 " pdb=" CB MET E 58 " pdb=" CG MET E 58 " ideal model delta sigma weight residual 114.10 122.99 -8.89 2.00e+00 2.50e-01 1.97e+01 angle pdb=" CA MET D 132 " pdb=" CB MET D 132 " pdb=" CG MET D 132 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CA LEU A 549 " pdb=" CB LEU A 549 " pdb=" CG LEU A 549 " ideal model delta sigma weight residual 116.30 128.51 -12.21 3.50e+00 8.16e-02 1.22e+01 angle pdb=" C MET E 58 " pdb=" CA MET E 58 " pdb=" CB MET E 58 " ideal model delta sigma weight residual 109.80 114.97 -5.17 1.61e+00 3.86e-01 1.03e+01 angle pdb=" CA MET A 532 " pdb=" CB MET A 532 " pdb=" CG MET A 532 " ideal model delta sigma weight residual 114.10 120.23 -6.13 2.00e+00 2.50e-01 9.39e+00 ... (remaining 9860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3892 17.85 - 35.70: 492 35.70 - 53.55: 125 53.55 - 71.41: 21 71.41 - 89.26: 8 Dihedral angle restraints: 4538 sinusoidal: 1903 harmonic: 2635 Sorted by residual: dihedral pdb=" CA PRO C 234 " pdb=" C PRO C 234 " pdb=" N PRO C 235 " pdb=" CA PRO C 235 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU B 188 " pdb=" C LEU B 188 " pdb=" N LYS B 189 " pdb=" CA LYS B 189 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ILE E 125 " pdb=" C ILE E 125 " pdb=" N ILE E 126 " pdb=" CA ILE E 126 " ideal model delta harmonic sigma weight residual 180.00 158.13 21.87 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 4535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 879 0.043 - 0.087: 213 0.087 - 0.130: 78 0.130 - 0.173: 3 0.173 - 0.216: 3 Chirality restraints: 1176 Sorted by residual: chirality pdb=" CG LEU B 56 " pdb=" CB LEU B 56 " pdb=" CD1 LEU B 56 " pdb=" CD2 LEU B 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE A 536 " pdb=" CA ILE A 536 " pdb=" CG1 ILE A 536 " pdb=" CG2 ILE A 536 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB VAL C 251 " pdb=" CA VAL C 251 " pdb=" CG1 VAL C 251 " pdb=" CG2 VAL C 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 1173 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 102 " 0.023 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C ASP B 102 " -0.078 2.00e-02 2.50e+03 pdb=" O ASP B 102 " 0.030 2.00e-02 2.50e+03 pdb=" N THR B 103 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 234 " -0.049 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO C 235 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 116 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" C ASP D 116 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP D 116 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS D 117 " -0.014 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 124 2.66 - 3.22: 7181 3.22 - 3.78: 11179 3.78 - 4.34: 14252 4.34 - 4.90: 23009 Nonbonded interactions: 55745 Sorted by model distance: nonbonded pdb=" OG SER C 273 " pdb=" O MET D 58 " model vdw 2.098 3.040 nonbonded pdb=" O ILE B 97 " pdb=" OG1 THR B 100 " model vdw 2.119 3.040 nonbonded pdb=" NZ LYS E 76 " pdb=" O MET F 58 " model vdw 2.170 3.120 nonbonded pdb=" O GLY B 106 " pdb=" OG1 THR B 109 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR C 179 " pdb=" OG SER C 182 " model vdw 2.220 3.040 ... (remaining 55740 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 'D' and resid 57 through 135) selection = (chain 'E' and resid 57 through 135) selection = (chain 'F' and resid 57 through 135) } 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: 0.010 Normalize map: mean=0, sd=1: 10.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.770 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.003 0.047 7290 Z= 0.153 Angle : 0.722 12.213 9865 Z= 0.375 Chirality : 0.043 0.216 1176 Planarity : 0.005 0.073 1290 Dihedral : 16.777 89.258 2822 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.89 % Favored : 94.77 % Rotamer: Outliers : 0.50 % Allowed : 26.69 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.54 (0.29), residues: 899 helix: 1.56 (0.26), residues: 435 sheet: 0.15 (0.52), residues: 97 loop : -1.05 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 134 TYR 0.009 0.001 TYR D 118 PHE 0.018 0.002 PHE C 70 TRP 0.004 0.001 TRP C 169 HIS 0.004 0.001 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7290) covalent geometry : angle 0.72181 ( 9865) hydrogen bonds : bond 0.15535 ( 392) hydrogen bonds : angle 6.85495 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.321 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: B 233 MET cc_start: 0.8573 (ttt) cc_final: 0.7989 (tpt) REVERT: B 270 LEU cc_start: 0.8772 (tp) cc_final: 0.8525 (mm) REVERT: C 67 MET cc_start: 0.9235 (mmt) cc_final: 0.8907 (mmm) REVERT: C 69 LEU cc_start: 0.9503 (mt) cc_final: 0.9272 (mt) REVERT: E 70 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7546 (ptp90) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.1052 time to fit residues: 13.2514 Evaluate side-chains 64 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain E residue 74 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.045537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.034452 restraints weight = 59884.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.035235 restraints weight = 36376.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.035781 restraints weight = 25752.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.036185 restraints weight = 20083.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.036462 restraints weight = 16745.309| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7290 Z= 0.135 Angle : 0.677 11.994 9865 Z= 0.343 Chirality : 0.043 0.178 1176 Planarity : 0.005 0.063 1290 Dihedral : 4.650 26.483 1003 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.67 % Favored : 94.99 % Rotamer: Outliers : 2.88 % Allowed : 24.31 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.66 (0.29), residues: 899 helix: 1.66 (0.25), residues: 437 sheet: 0.06 (0.54), residues: 92 loop : -0.96 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 121 TYR 0.006 0.001 TYR C 38 PHE 0.011 0.001 PHE C 215 TRP 0.004 0.001 TRP A 554 HIS 0.002 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7290) covalent geometry : angle 0.67728 ( 9865) hydrogen bonds : bond 0.03862 ( 392) hydrogen bonds : angle 5.07341 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9293 (ttt) cc_final: 0.8476 (tpt) REVERT: B 270 LEU cc_start: 0.8924 (tp) cc_final: 0.8665 (mm) REVERT: B 278 MET cc_start: 0.3506 (mmt) cc_final: 0.2232 (mmt) REVERT: C 67 MET cc_start: 0.8936 (mmt) cc_final: 0.8546 (mmm) REVERT: C 170 LYS cc_start: 0.9660 (tppp) cc_final: 0.9359 (tppp) REVERT: E 68 LEU cc_start: 0.9580 (tp) cc_final: 0.9208 (mm) REVERT: E 71 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8412 (p) REVERT: E 77 GLU cc_start: 0.9087 (mp0) cc_final: 0.8838 (mp0) REVERT: F 116 ASP cc_start: 0.7739 (t0) cc_final: 0.7433 (t0) outliers start: 23 outliers final: 16 residues processed: 96 average time/residue: 0.0970 time to fit residues: 12.5483 Evaluate side-chains 79 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 0.0370 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN C 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.045173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.034267 restraints weight = 59831.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.035039 restraints weight = 36116.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.035587 restraints weight = 25532.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.035987 restraints weight = 19786.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.036258 restraints weight = 16432.216| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7290 Z= 0.123 Angle : 0.624 8.968 9865 Z= 0.318 Chirality : 0.042 0.173 1176 Planarity : 0.004 0.060 1290 Dihedral : 4.396 23.116 1000 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.12 % Favored : 94.55 % Rotamer: Outliers : 4.01 % Allowed : 22.93 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.75 (0.29), residues: 899 helix: 1.72 (0.26), residues: 436 sheet: 0.17 (0.56), residues: 92 loop : -0.91 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 121 TYR 0.005 0.001 TYR C 38 PHE 0.011 0.001 PHE C 65 TRP 0.005 0.001 TRP A 554 HIS 0.003 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7290) covalent geometry : angle 0.62350 ( 9865) hydrogen bonds : bond 0.03542 ( 392) hydrogen bonds : angle 4.74660 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9184 (ttt) cc_final: 0.8792 (ttt) REVERT: B 270 LEU cc_start: 0.8961 (tp) cc_final: 0.8693 (mm) REVERT: B 278 MET cc_start: 0.4069 (mmt) cc_final: 0.2931 (mmt) REVERT: C 67 MET cc_start: 0.8920 (mmt) cc_final: 0.8532 (mmm) REVERT: C 108 LYS cc_start: 0.9461 (mmtt) cc_final: 0.9183 (mmtt) REVERT: C 170 LYS cc_start: 0.9669 (tppp) cc_final: 0.9390 (tppp) REVERT: D 73 MET cc_start: 0.8061 (tmm) cc_final: 0.7810 (tmm) REVERT: E 77 GLU cc_start: 0.9105 (mp0) cc_final: 0.8796 (mp0) outliers start: 32 outliers final: 18 residues processed: 91 average time/residue: 0.0997 time to fit residues: 12.2791 Evaluate side-chains 77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 59 optimal weight: 0.0270 chunk 47 optimal weight: 2.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.045235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.034234 restraints weight = 60886.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.035036 restraints weight = 36706.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.035592 restraints weight = 25673.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.036004 restraints weight = 19855.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.036242 restraints weight = 16461.862| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 7290 Z= 0.113 Angle : 0.608 9.941 9865 Z= 0.310 Chirality : 0.042 0.162 1176 Planarity : 0.004 0.058 1290 Dihedral : 4.266 22.755 1000 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.12 % Favored : 95.55 % Rotamer: Outliers : 4.14 % Allowed : 22.43 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.82 (0.29), residues: 899 helix: 1.78 (0.26), residues: 435 sheet: -0.05 (0.56), residues: 84 loop : -0.77 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 80 TYR 0.005 0.001 TYR B 76 PHE 0.012 0.001 PHE C 131 TRP 0.005 0.001 TRP A 554 HIS 0.002 0.000 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7290) covalent geometry : angle 0.60825 ( 9865) hydrogen bonds : bond 0.03321 ( 392) hydrogen bonds : angle 4.54613 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9186 (ttt) cc_final: 0.8893 (ttt) REVERT: B 270 LEU cc_start: 0.8977 (tp) cc_final: 0.8706 (mm) REVERT: B 278 MET cc_start: 0.4424 (mmt) cc_final: 0.3761 (mmt) REVERT: C 67 MET cc_start: 0.8943 (mmt) cc_final: 0.8569 (mmm) REVERT: C 170 LYS cc_start: 0.9666 (tppp) cc_final: 0.9364 (tppp) REVERT: D 63 LYS cc_start: 0.9181 (tppt) cc_final: 0.8954 (tppt) REVERT: D 73 MET cc_start: 0.8142 (tmm) cc_final: 0.7828 (tmm) REVERT: E 77 GLU cc_start: 0.9100 (mp0) cc_final: 0.8810 (mp0) REVERT: F 97 LEU cc_start: 0.9311 (mp) cc_final: 0.8941 (mp) REVERT: F 116 ASP cc_start: 0.7759 (t0) cc_final: 0.7528 (t0) outliers start: 33 outliers final: 22 residues processed: 92 average time/residue: 0.0993 time to fit residues: 12.2779 Evaluate side-chains 82 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.044099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.033383 restraints weight = 60458.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.034135 restraints weight = 36200.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034658 restraints weight = 25524.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.035047 restraints weight = 19824.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035315 restraints weight = 16441.558| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7290 Z= 0.185 Angle : 0.637 7.864 9865 Z= 0.328 Chirality : 0.042 0.155 1176 Planarity : 0.004 0.058 1290 Dihedral : 4.347 24.518 1000 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.89 % Favored : 94.77 % Rotamer: Outliers : 4.39 % Allowed : 23.93 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.88 (0.30), residues: 899 helix: 1.82 (0.26), residues: 433 sheet: -0.08 (0.57), residues: 85 loop : -0.69 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 121 TYR 0.014 0.002 TYR C 38 PHE 0.016 0.002 PHE C 131 TRP 0.009 0.002 TRP A 554 HIS 0.004 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7290) covalent geometry : angle 0.63745 ( 9865) hydrogen bonds : bond 0.03521 ( 392) hydrogen bonds : angle 4.61885 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 59 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9218 (ttt) cc_final: 0.8942 (ttt) REVERT: B 270 LEU cc_start: 0.9065 (tp) cc_final: 0.8787 (mm) REVERT: B 278 MET cc_start: 0.5149 (mmt) cc_final: 0.4384 (mmt) REVERT: C 67 MET cc_start: 0.9072 (mmt) cc_final: 0.8641 (mmm) REVERT: C 170 LYS cc_start: 0.9730 (tppp) cc_final: 0.9444 (tppp) REVERT: D 63 LYS cc_start: 0.9182 (tppt) cc_final: 0.8836 (tppt) REVERT: D 73 MET cc_start: 0.8336 (tmm) cc_final: 0.8112 (tmm) REVERT: E 77 GLU cc_start: 0.9090 (mp0) cc_final: 0.8684 (mp0) REVERT: F 59 ASP cc_start: 0.8641 (t0) cc_final: 0.8026 (t0) REVERT: F 81 LEU cc_start: 0.9354 (mt) cc_final: 0.9124 (mt) REVERT: F 116 ASP cc_start: 0.8453 (t0) cc_final: 0.8249 (t0) REVERT: F 123 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.8920 (p) outliers start: 35 outliers final: 24 residues processed: 91 average time/residue: 0.0933 time to fit residues: 11.6517 Evaluate side-chains 79 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 TYR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 81 optimal weight: 0.0770 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.044884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.033931 restraints weight = 61140.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.034759 restraints weight = 35904.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035331 restraints weight = 24909.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035725 restraints weight = 19171.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.036015 restraints weight = 15840.107| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 7290 Z= 0.111 Angle : 0.613 8.557 9865 Z= 0.310 Chirality : 0.041 0.139 1176 Planarity : 0.004 0.057 1290 Dihedral : 4.232 23.989 1000 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.67 % Favored : 94.99 % Rotamer: Outliers : 3.76 % Allowed : 25.44 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.90 (0.30), residues: 899 helix: 1.90 (0.26), residues: 432 sheet: -0.13 (0.60), residues: 78 loop : -0.74 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 80 TYR 0.008 0.001 TYR D 118 PHE 0.012 0.001 PHE B 234 TRP 0.006 0.001 TRP A 554 HIS 0.003 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7290) covalent geometry : angle 0.61338 ( 9865) hydrogen bonds : bond 0.03276 ( 392) hydrogen bonds : angle 4.43403 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.8185 (tmm) cc_final: 0.7816 (tmm) REVERT: B 233 MET cc_start: 0.9215 (ttt) cc_final: 0.8928 (ttt) REVERT: B 270 LEU cc_start: 0.9053 (tp) cc_final: 0.8788 (mm) REVERT: B 278 MET cc_start: 0.5114 (mmt) cc_final: 0.4309 (mmt) REVERT: C 67 MET cc_start: 0.8998 (mmt) cc_final: 0.8577 (mmm) REVERT: D 63 LYS cc_start: 0.9219 (tppt) cc_final: 0.8975 (tppt) REVERT: D 73 MET cc_start: 0.8439 (tmm) cc_final: 0.8148 (tmm) REVERT: E 77 GLU cc_start: 0.9069 (mp0) cc_final: 0.8665 (mp0) REVERT: F 59 ASP cc_start: 0.8541 (t0) cc_final: 0.7853 (t0) REVERT: F 73 MET cc_start: 0.8246 (ppp) cc_final: 0.6628 (ppp) REVERT: F 116 ASP cc_start: 0.8369 (t0) cc_final: 0.8075 (t0) outliers start: 30 outliers final: 24 residues processed: 85 average time/residue: 0.0926 time to fit residues: 10.8260 Evaluate side-chains 81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 0.7980 chunk 11 optimal weight: 0.0270 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.045232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.034205 restraints weight = 61053.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.035019 restraints weight = 35925.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.035584 restraints weight = 24960.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.035992 restraints weight = 19261.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.036280 restraints weight = 15894.898| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 7290 Z= 0.109 Angle : 0.629 11.302 9865 Z= 0.313 Chirality : 0.043 0.190 1176 Planarity : 0.004 0.057 1290 Dihedral : 4.137 23.129 1000 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.67 % Favored : 94.99 % Rotamer: Outliers : 3.51 % Allowed : 26.32 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.76 (0.30), residues: 899 helix: 1.70 (0.26), residues: 439 sheet: -0.25 (0.62), residues: 73 loop : -0.73 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 535 TYR 0.006 0.001 TYR D 118 PHE 0.013 0.001 PHE B 234 TRP 0.005 0.001 TRP A 554 HIS 0.002 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7290) covalent geometry : angle 0.62862 ( 9865) hydrogen bonds : bond 0.03207 ( 392) hydrogen bonds : angle 4.41463 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9202 (ttt) cc_final: 0.8905 (ttt) REVERT: B 270 LEU cc_start: 0.9126 (tp) cc_final: 0.8838 (mm) REVERT: B 278 MET cc_start: 0.4960 (mmt) cc_final: 0.4167 (mmt) REVERT: D 63 LYS cc_start: 0.9221 (tppt) cc_final: 0.8941 (tppt) REVERT: D 73 MET cc_start: 0.8605 (tmm) cc_final: 0.8342 (tmm) REVERT: E 77 GLU cc_start: 0.9065 (mp0) cc_final: 0.8747 (mp0) REVERT: F 73 MET cc_start: 0.8975 (ppp) cc_final: 0.8746 (ppp) REVERT: F 116 ASP cc_start: 0.8497 (t0) cc_final: 0.8180 (t0) outliers start: 28 outliers final: 23 residues processed: 87 average time/residue: 0.0918 time to fit residues: 11.0384 Evaluate side-chains 78 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.045334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.034391 restraints weight = 61542.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035232 restraints weight = 35604.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035818 restraints weight = 24446.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.036221 restraints weight = 18684.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.036513 restraints weight = 15409.510| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7290 Z= 0.120 Angle : 0.669 13.314 9865 Z= 0.326 Chirality : 0.043 0.238 1176 Planarity : 0.004 0.057 1290 Dihedral : 4.106 23.131 1000 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.67 % Favored : 94.99 % Rotamer: Outliers : 3.26 % Allowed : 27.07 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.77 (0.30), residues: 899 helix: 1.67 (0.26), residues: 439 sheet: -0.26 (0.63), residues: 73 loop : -0.66 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 271 TYR 0.007 0.001 TYR D 118 PHE 0.013 0.001 PHE B 234 TRP 0.009 0.001 TRP A 554 HIS 0.002 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7290) covalent geometry : angle 0.66864 ( 9865) hydrogen bonds : bond 0.03237 ( 392) hydrogen bonds : angle 4.43284 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6832 (m-30) REVERT: B 113 MET cc_start: 0.8574 (tmm) cc_final: 0.8060 (ppp) REVERT: B 233 MET cc_start: 0.9236 (ttt) cc_final: 0.8903 (ttt) REVERT: B 270 LEU cc_start: 0.9142 (tp) cc_final: 0.8855 (mm) REVERT: B 278 MET cc_start: 0.5142 (mmt) cc_final: 0.4333 (mmt) REVERT: D 63 LYS cc_start: 0.9133 (tppt) cc_final: 0.8842 (tppt) REVERT: D 73 MET cc_start: 0.8459 (tmm) cc_final: 0.7666 (tmm) REVERT: E 77 GLU cc_start: 0.9064 (mp0) cc_final: 0.8746 (mp0) REVERT: F 116 ASP cc_start: 0.8619 (t0) cc_final: 0.8257 (t0) outliers start: 26 outliers final: 23 residues processed: 81 average time/residue: 0.1012 time to fit residues: 11.0961 Evaluate side-chains 79 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.045664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.034833 restraints weight = 60528.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.035682 restraints weight = 34787.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036263 restraints weight = 23753.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.036685 restraints weight = 18107.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.036973 restraints weight = 14836.132| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7290 Z= 0.112 Angle : 0.666 11.096 9865 Z= 0.328 Chirality : 0.043 0.214 1176 Planarity : 0.004 0.057 1290 Dihedral : 4.054 22.609 1000 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.67 % Favored : 94.99 % Rotamer: Outliers : 3.51 % Allowed : 27.07 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.76 (0.30), residues: 899 helix: 1.67 (0.26), residues: 439 sheet: -0.27 (0.63), residues: 73 loop : -0.67 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 80 TYR 0.006 0.001 TYR D 118 PHE 0.014 0.001 PHE B 234 TRP 0.008 0.001 TRP A 554 HIS 0.002 0.000 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7290) covalent geometry : angle 0.66572 ( 9865) hydrogen bonds : bond 0.03211 ( 392) hydrogen bonds : angle 4.42182 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.8296 (tmm) cc_final: 0.7966 (ppp) REVERT: B 233 MET cc_start: 0.9147 (ttt) cc_final: 0.8924 (ttt) REVERT: B 270 LEU cc_start: 0.9078 (tp) cc_final: 0.8787 (mm) REVERT: B 278 MET cc_start: 0.4502 (mmt) cc_final: 0.3710 (mmt) REVERT: D 73 MET cc_start: 0.8575 (tmm) cc_final: 0.7859 (tmm) REVERT: D 110 GLU cc_start: 0.9063 (pt0) cc_final: 0.8575 (pm20) REVERT: F 116 ASP cc_start: 0.8439 (t0) cc_final: 0.8072 (t0) outliers start: 28 outliers final: 22 residues processed: 86 average time/residue: 0.0906 time to fit residues: 10.7148 Evaluate side-chains 79 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.044805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.034051 restraints weight = 60812.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.034901 restraints weight = 34845.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.035473 restraints weight = 23836.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.035874 restraints weight = 18211.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.036160 restraints weight = 14945.898| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7290 Z= 0.152 Angle : 0.720 11.189 9865 Z= 0.354 Chirality : 0.043 0.201 1176 Planarity : 0.004 0.057 1290 Dihedral : 4.140 23.177 1000 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.89 % Favored : 94.77 % Rotamer: Outliers : 3.01 % Allowed : 27.57 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.81 (0.29), residues: 899 helix: 1.63 (0.26), residues: 438 sheet: 0.27 (0.62), residues: 73 loop : -0.66 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 121 TYR 0.009 0.001 TYR D 118 PHE 0.014 0.001 PHE B 234 TRP 0.005 0.001 TRP A 554 HIS 0.002 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7290) covalent geometry : angle 0.71974 ( 9865) hydrogen bonds : bond 0.03368 ( 392) hydrogen bonds : angle 4.57692 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.8381 (tmm) cc_final: 0.7938 (ppp) REVERT: B 233 MET cc_start: 0.9153 (ttt) cc_final: 0.8945 (ttt) REVERT: B 270 LEU cc_start: 0.9099 (tp) cc_final: 0.8779 (mm) REVERT: B 278 MET cc_start: 0.4803 (mmt) cc_final: 0.3984 (mmt) REVERT: D 73 MET cc_start: 0.8473 (tmm) cc_final: 0.7666 (tmm) REVERT: F 116 ASP cc_start: 0.8549 (t0) cc_final: 0.8166 (t0) outliers start: 24 outliers final: 23 residues processed: 80 average time/residue: 0.0901 time to fit residues: 10.0198 Evaluate side-chains 80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 29 optimal weight: 0.1980 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.044692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.033946 restraints weight = 61695.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034749 restraints weight = 36072.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.035311 restraints weight = 24903.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035708 restraints weight = 19156.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.035977 restraints weight = 15822.161| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7290 Z= 0.142 Angle : 0.712 10.978 9865 Z= 0.356 Chirality : 0.044 0.205 1176 Planarity : 0.004 0.057 1290 Dihedral : 4.157 23.613 1000 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.45 % Favored : 95.22 % Rotamer: Outliers : 3.26 % Allowed : 27.19 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.77 (0.30), residues: 899 helix: 1.58 (0.26), residues: 439 sheet: 0.27 (0.62), residues: 73 loop : -0.67 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 70 TYR 0.009 0.001 TYR D 118 PHE 0.015 0.001 PHE B 234 TRP 0.007 0.001 TRP A 554 HIS 0.002 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7290) covalent geometry : angle 0.71158 ( 9865) hydrogen bonds : bond 0.03367 ( 392) hydrogen bonds : angle 4.59373 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.14 seconds wall clock time: 31 minutes 22.36 seconds (1882.36 seconds total)