Starting phenix.real_space_refine on Wed Sep 17 23:34:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mn6_48414/09_2025/9mn6_48414.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mn6_48414/09_2025/9mn6_48414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mn6_48414/09_2025/9mn6_48414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mn6_48414/09_2025/9mn6_48414.map" model { file = "/net/cci-nas-00/data/ceres_data/9mn6_48414/09_2025/9mn6_48414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mn6_48414/09_2025/9mn6_48414.cif" } resolution = 2.71 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= 0.001 sd= 0.022 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: 6 Type Number sf(0) Gaussians P 69 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 7338 2.51 5 N 2123 2.21 5 O 2261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11855 Number of models: 1 Model: "" Number of chains: 6 Chain: "N" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 618 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 133 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 5} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 7953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7953 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 64, 'TRANS': 932} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2507 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 19, 'TRANS': 289} Chain breaks: 1 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.54, per 1000 atoms: 0.21 Number of scatterers: 11855 At special positions: 0 Unit cell: (97.82, 129.94, 110.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 69 15.00 Mg 1 11.99 O 2261 8.00 N 2123 7.00 C 7338 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: 1.02 Conformation dependent library (CDL) restraints added in 459.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2478 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 9 sheets defined 59.5% alpha, 6.0% beta 21 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'E' and resid 220 through 237 Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.797A pdb=" N GLN E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.964A pdb=" N VAL E 267 " --> pdb=" O MET E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 291 removed outlier: 3.737A pdb=" N TYR E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY E 291 " --> pdb=" O VAL E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 removed outlier: 3.549A pdb=" N TYR E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 327 removed outlier: 3.938A pdb=" N ILE E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 Processing helix chain 'E' and resid 340 through 355 removed outlier: 4.020A pdb=" N LYS E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 410 Processing helix chain 'E' and resid 424 through 462 Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 475 through 489 Processing helix chain 'E' and resid 497 through 520 Processing helix chain 'E' and resid 521 through 538 removed outlier: 3.701A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 532 " --> pdb=" O ASN E 528 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N CYS E 535 " --> pdb=" O ARG E 531 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU E 536 " --> pdb=" O LYS E 532 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU E 537 " --> pdb=" O TYR E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 556 Processing helix chain 'E' and resid 568 through 587 Processing helix chain 'E' and resid 624 through 635 removed outlier: 3.604A pdb=" N ALA E 635 " --> pdb=" O LEU E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 687 Processing helix chain 'E' and resid 692 through 704 Processing helix chain 'E' and resid 710 through 723 Processing helix chain 'E' and resid 726 through 730 Processing helix chain 'E' and resid 734 through 738 Processing helix chain 'E' and resid 760 through 789 Processing helix chain 'E' and resid 818 through 824 Processing helix chain 'E' and resid 837 through 850 removed outlier: 3.634A pdb=" N GLY E 850 " --> pdb=" O VAL E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 867 through 877 Processing helix chain 'E' and resid 884 through 888 Processing helix chain 'E' and resid 890 through 906 Processing helix chain 'E' and resid 925 through 936 Processing helix chain 'E' and resid 939 through 944 Processing helix chain 'E' and resid 954 through 973 removed outlier: 3.781A pdb=" N GLY E 958 " --> pdb=" O ASP E 954 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 982 removed outlier: 3.520A pdb=" N GLN E 979 " --> pdb=" O MET E 975 " (cutoff:3.500A) Processing helix chain 'E' and resid 983 through 985 No H-bonds generated for 'chain 'E' and resid 983 through 985' Processing helix chain 'E' and resid 986 through 998 removed outlier: 3.903A pdb=" N VAL E 990 " --> pdb=" O THR E 986 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN E 992 " --> pdb=" O LYS E 988 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N THR E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL E 998 " --> pdb=" O VAL E 994 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1016 removed outlier: 3.605A pdb=" N ARG E1013 " --> pdb=" O GLN E1009 " (cutoff:3.500A) Processing helix chain 'E' and resid 1021 through 1023 No H-bonds generated for 'chain 'E' and resid 1021 through 1023' Processing helix chain 'E' and resid 1024 through 1040 Processing helix chain 'E' and resid 1044 through 1064 removed outlier: 3.744A pdb=" N MET E1064 " --> pdb=" O LEU E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1111 through 1141 Proline residue: E1120 - end of helix removed outlier: 3.705A pdb=" N ILE E1124 " --> pdb=" O PRO E1120 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG E1141 " --> pdb=" O LEU E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1176 Processing helix chain 'E' and resid 1178 through 1192 Processing helix chain 'E' and resid 1194 through 1196 No H-bonds generated for 'chain 'E' and resid 1194 through 1196' Processing helix chain 'E' and resid 1197 through 1209 removed outlier: 5.733A pdb=" N GLN E1203 " --> pdb=" O LEU E1199 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU E1204 " --> pdb=" O GLU E1200 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN E1209 " --> pdb=" O LYS E1205 " (cutoff:3.500A) Processing helix chain 'E' and resid 1218 through 1225 Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.916A pdb=" N GLY B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 126 through 129 removed outlier: 3.863A pdb=" N PHE B 129 " --> pdb=" O ASP B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 126 through 129' Processing helix chain 'B' and resid 130 through 140 removed outlier: 4.075A pdb=" N GLU B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.647A pdb=" N LEU B 154 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 199 through 213 Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.727A pdb=" N LYS B 219 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 221 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.761A pdb=" N VAL B 252 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.719A pdb=" N LEU B 307 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE B 308 " --> pdb=" O GLN B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.638A pdb=" N PHE B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.768A pdb=" N SER B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 366 through 379 removed outlier: 3.589A pdb=" N LYS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.589A pdb=" N ASP B 395 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 411 through 415 Processing sheet with id=AA2, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.545A pdb=" N GLU E 495 " --> pdb=" O LEU E 621 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 588 through 589 Processing sheet with id=AA4, first strand: chain 'E' and resid 794 through 795 Processing sheet with id=AA5, first strand: chain 'E' and resid 798 through 800 Processing sheet with id=AA6, first strand: chain 'E' and resid 831 through 832 Processing sheet with id=AA7, first strand: chain 'E' and resid 1147 through 1149 Processing sheet with id=AA8, first strand: chain 'E' and resid 1069 through 1071 Processing sheet with id=AA9, first strand: chain 'B' and resid 147 through 148 removed outlier: 7.779A pdb=" N ILE B 147 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ALA B 122 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU B 99 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 123 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLU B 101 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL B 191 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N PHE B 228 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY B 193 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU B 296 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET B 265 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 298 " --> pdb=" O LEU B 263 " (cutoff:3.500A) 542 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.39 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: 3145 1.34 - 1.45: 2471 1.45 - 1.57: 6426 1.57 - 1.69: 135 1.69 - 1.81: 96 Bond restraints: 12273 Sorted by residual: bond pdb=" C PRO B 164 " pdb=" N PRO B 165 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.20e-02 6.94e+03 1.73e+01 bond pdb=" CA ASN E 614 " pdb=" CB ASN E 614 " ideal model delta sigma weight residual 1.522 1.581 -0.059 1.86e-02 2.89e+03 1.01e+01 bond pdb=" N ASP E 237 " pdb=" CA ASP E 237 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.32e-02 5.74e+03 7.12e+00 bond pdb=" N LEU E 241 " pdb=" CA LEU E 241 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.76e+00 bond pdb=" N CYS E 233 " pdb=" CA CYS E 233 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.08e+00 ... (remaining 12268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 16660 3.06 - 6.13: 225 6.13 - 9.19: 34 9.19 - 12.26: 6 12.26 - 15.32: 1 Bond angle restraints: 16926 Sorted by residual: angle pdb=" CA ASP E 237 " pdb=" CB ASP E 237 " pdb=" CG ASP E 237 " ideal model delta sigma weight residual 112.60 118.25 -5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" C HIS E1150 " pdb=" N ASP E1151 " pdb=" CA ASP E1151 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.94e+01 angle pdb=" O3' DA N 41 " pdb=" P DA N 42 " pdb=" O5' DA N 42 " ideal model delta sigma weight residual 104.00 111.62 -7.62 1.50e+00 4.44e-01 2.58e+01 angle pdb=" N PRO B 164 " pdb=" CA PRO B 164 " pdb=" C PRO B 164 " ideal model delta sigma weight residual 110.70 116.32 -5.62 1.22e+00 6.72e-01 2.12e+01 angle pdb=" CA LEU B 80 " pdb=" CB LEU B 80 " pdb=" CG LEU B 80 " ideal model delta sigma weight residual 116.30 131.62 -15.32 3.50e+00 8.16e-02 1.92e+01 ... (remaining 16921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 6966 35.73 - 71.47: 330 71.47 - 107.20: 5 107.20 - 142.93: 2 142.93 - 178.67: 2 Dihedral angle restraints: 7305 sinusoidal: 3488 harmonic: 3817 Sorted by residual: dihedral pdb=" CA SER E1148 " pdb=" C SER E1148 " pdb=" N VAL E1149 " pdb=" CA VAL E1149 " ideal model delta harmonic sigma weight residual 180.00 149.96 30.04 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA MET B 194 " pdb=" C MET B 194 " pdb=" N PHE B 195 " pdb=" CA PHE B 195 " ideal model delta harmonic sigma weight residual 180.00 150.07 29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA GLN E 252 " pdb=" C GLN E 252 " pdb=" N ARG E 253 " pdb=" CA ARG E 253 " ideal model delta harmonic sigma weight residual 180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 7302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1846 0.132 - 0.264: 28 0.264 - 0.397: 1 0.397 - 0.529: 3 0.529 - 0.661: 4 Chirality restraints: 1882 Sorted by residual: chirality pdb=" P DG N 39 " pdb=" OP1 DG N 39 " pdb=" OP2 DG N 39 " pdb=" O5' DG N 39 " both_signs ideal model delta sigma weight residual True 2.35 -3.01 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" P DA N 42 " pdb=" OP1 DA N 42 " pdb=" OP2 DA N 42 " pdb=" O5' DA N 42 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.49e+00 chirality pdb=" P DG N 44 " pdb=" OP1 DG N 44 " pdb=" OP2 DG N 44 " pdb=" O5' DG N 44 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.00e+00 ... (remaining 1879 not shown) Planarity restraints: 1937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 803 " -0.382 9.50e-02 1.11e+02 1.72e-01 1.91e+01 pdb=" NE ARG E 803 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG E 803 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG E 803 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG E 803 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 103 " -0.051 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO B 104 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 104 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 104 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS E1150 " 0.013 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C HIS E1150 " -0.048 2.00e-02 2.50e+03 pdb=" O HIS E1150 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP E1151 " 0.016 2.00e-02 2.50e+03 ... (remaining 1934 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 72 2.59 - 3.17: 9150 3.17 - 3.75: 19365 3.75 - 4.32: 26187 4.32 - 4.90: 41875 Nonbonded interactions: 96649 Sorted by model distance: nonbonded pdb=" O GLY E 923 " pdb="MG MG E1302 " model vdw 2.016 2.170 nonbonded pdb=" O2A ATP E1301 " pdb="MG MG E1302 " model vdw 2.021 2.170 nonbonded pdb=" OD2 ASP E 922 " pdb="MG MG E1302 " model vdw 2.056 2.170 nonbonded pdb=" O LYS B 236 " pdb=" OG SER B 251 " model vdw 2.229 3.040 nonbonded pdb=" O VAL E1025 " pdb=" OG SER E1029 " model vdw 2.237 3.040 ... (remaining 96644 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5004 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 : 0.005 0.062 12273 Z= 0.228 Angle : 0.907 15.321 16926 Z= 0.484 Chirality : 0.058 0.661 1882 Planarity : 0.009 0.172 1937 Dihedral : 17.858 178.665 4827 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.17 % Allowed : 0.35 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.21), residues: 1298 helix: -0.17 (0.18), residues: 691 sheet: -1.59 (0.51), residues: 90 loop : -0.80 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 803 TYR 0.022 0.002 TYR B 88 PHE 0.027 0.003 PHE E 470 TRP 0.026 0.002 TRP E1026 HIS 0.012 0.002 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00477 (12273) covalent geometry : angle 0.90719 (16926) hydrogen bonds : bond 0.15019 ( 595) hydrogen bonds : angle 5.90289 ( 1654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 342 GLU cc_start: 0.6326 (tm-30) cc_final: 0.6112 (tm-30) REVERT: E 515 GLN cc_start: 0.6622 (tp40) cc_final: 0.6258 (tp40) REVERT: E 632 GLU cc_start: 0.7085 (mp0) cc_final: 0.6615 (mp0) REVERT: E 943 SER cc_start: 0.7385 (m) cc_final: 0.7122 (m) REVERT: E 947 GLU cc_start: 0.7336 (tt0) cc_final: 0.7133 (tt0) REVERT: E 951 VAL cc_start: 0.8044 (m) cc_final: 0.7820 (t) REVERT: B 266 GLU cc_start: 0.7249 (tp30) cc_final: 0.7017 (tp30) REVERT: B 295 LYS cc_start: 0.6421 (ttmm) cc_final: 0.5952 (ttmm) REVERT: B 309 THR cc_start: 0.6516 (p) cc_final: 0.6280 (p) outliers start: 2 outliers final: 1 residues processed: 243 average time/residue: 0.6319 time to fit residues: 165.1359 Evaluate side-chains 210 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0030 chunk 91 optimal weight: 0.0270 chunk 55 optimal weight: 0.4980 overall best weight: 0.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 GLN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN E 304 GLN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS E 969 GLN E 979 GLN E1035 GLN E1103 ASN E1138 HIS E1165 GLN B 97 HIS B 294 GLN B 311 ASN B 322 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.184281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.156226 restraints weight = 16518.138| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.80 r_work: 0.3932 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 12273 Z= 0.148 Angle : 0.629 7.839 16926 Z= 0.328 Chirality : 0.040 0.206 1882 Planarity : 0.006 0.052 1937 Dihedral : 19.964 178.282 2202 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.57 % Allowed : 10.14 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.38 (0.23), residues: 1298 helix: 0.93 (0.19), residues: 701 sheet: -1.36 (0.54), residues: 80 loop : -0.27 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 331 TYR 0.014 0.001 TYR E1227 PHE 0.017 0.001 PHE B 370 TRP 0.011 0.001 TRP B 205 HIS 0.011 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00335 (12273) covalent geometry : angle 0.62926 (16926) hydrogen bonds : bond 0.04532 ( 595) hydrogen bonds : angle 4.37025 ( 1654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 342 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7175 (tm-30) REVERT: E 792 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7650 (mtp180) REVERT: E 1051 GLN cc_start: 0.6876 (tt0) cc_final: 0.6650 (tt0) REVERT: B 265 MET cc_start: 0.8003 (ttt) cc_final: 0.7623 (tpt) REVERT: B 295 LYS cc_start: 0.7459 (ttmm) cc_final: 0.6700 (ttmm) outliers start: 18 outliers final: 9 residues processed: 219 average time/residue: 0.6262 time to fit residues: 147.9161 Evaluate side-chains 212 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 1002 THR Chi-restraints excluded: chain E residue 1023 GLU Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain B residue 224 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 97 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 0.0570 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 528 ASN E 585 GLN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS E 992 GLN E1165 GLN B 311 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.181621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.153079 restraints weight = 16512.549| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.79 r_work: 0.3890 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12273 Z= 0.171 Angle : 0.619 9.658 16926 Z= 0.322 Chirality : 0.040 0.200 1882 Planarity : 0.005 0.055 1937 Dihedral : 19.806 179.740 2202 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.27 % Allowed : 11.54 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.60 (0.23), residues: 1298 helix: 1.21 (0.19), residues: 709 sheet: -1.30 (0.48), residues: 90 loop : -0.34 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 331 TYR 0.017 0.002 TYR B 247 PHE 0.024 0.002 PHE B 370 TRP 0.025 0.002 TRP E 441 HIS 0.012 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00392 (12273) covalent geometry : angle 0.61931 (16926) hydrogen bonds : bond 0.04333 ( 595) hydrogen bonds : angle 4.12846 ( 1654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 289 ASP cc_start: 0.7358 (t0) cc_final: 0.7139 (t0) REVERT: E 342 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7168 (tm-30) REVERT: E 787 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: E 792 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7771 (mtp180) REVERT: B 259 GLU cc_start: 0.5498 (mp0) cc_final: 0.5220 (mp0) REVERT: B 264 HIS cc_start: 0.7304 (t70) cc_final: 0.7058 (t70) REVERT: B 265 MET cc_start: 0.8130 (ttt) cc_final: 0.7912 (ttt) REVERT: B 295 LYS cc_start: 0.7548 (ttmm) cc_final: 0.6824 (ttmm) REVERT: B 309 THR cc_start: 0.7204 (p) cc_final: 0.6997 (p) outliers start: 26 outliers final: 11 residues processed: 225 average time/residue: 0.6174 time to fit residues: 150.1796 Evaluate side-chains 220 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 224 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN E 369 ASN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 844 HIS E 920 HIS ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1165 GLN B 311 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.181449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.152813 restraints weight = 16502.924| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.78 r_work: 0.3886 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12273 Z= 0.162 Angle : 0.601 8.353 16926 Z= 0.311 Chirality : 0.040 0.191 1882 Planarity : 0.005 0.046 1937 Dihedral : 19.641 179.239 2202 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.88 % Allowed : 12.85 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.23), residues: 1298 helix: 1.47 (0.20), residues: 702 sheet: -1.38 (0.47), residues: 90 loop : -0.16 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E1034 TYR 0.015 0.001 TYR B 247 PHE 0.020 0.002 PHE B 195 TRP 0.028 0.002 TRP E 441 HIS 0.010 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00375 (12273) covalent geometry : angle 0.60129 (16926) hydrogen bonds : bond 0.04095 ( 595) hydrogen bonds : angle 4.03338 ( 1654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 277 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7446 (m-10) REVERT: E 289 ASP cc_start: 0.7380 (t0) cc_final: 0.7132 (t0) REVERT: E 323 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6508 (tpp) REVERT: E 471 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8574 (mp) REVERT: E 787 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: E 792 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7812 (mtp180) REVERT: E 801 ASP cc_start: 0.8046 (p0) cc_final: 0.7770 (p0) REVERT: E 1040 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8158 (mp) REVERT: B 259 GLU cc_start: 0.5605 (mp0) cc_final: 0.5141 (mp0) REVERT: B 264 HIS cc_start: 0.7339 (t70) cc_final: 0.7105 (t70) REVERT: B 265 MET cc_start: 0.8135 (ttt) cc_final: 0.7912 (ttt) REVERT: B 266 GLU cc_start: 0.8437 (tp30) cc_final: 0.8022 (tp30) REVERT: B 295 LYS cc_start: 0.7562 (ttmm) cc_final: 0.6843 (ttmm) REVERT: B 309 THR cc_start: 0.7198 (p) cc_final: 0.6981 (p) outliers start: 33 outliers final: 13 residues processed: 226 average time/residue: 0.6477 time to fit residues: 157.8373 Evaluate side-chains 231 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 976 ARG Chi-restraints excluded: chain E residue 1040 LEU Chi-restraints excluded: chain E residue 1230 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 365 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 52 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 ASN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1165 GLN B 311 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.180639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.151807 restraints weight = 16347.183| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.77 r_work: 0.3870 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12273 Z= 0.180 Angle : 0.619 8.332 16926 Z= 0.321 Chirality : 0.040 0.193 1882 Planarity : 0.005 0.047 1937 Dihedral : 19.583 179.087 2202 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.50 % Allowed : 12.06 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.87 (0.23), residues: 1298 helix: 1.50 (0.20), residues: 700 sheet: -1.40 (0.48), residues: 90 loop : -0.25 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 331 TYR 0.015 0.001 TYR E1227 PHE 0.021 0.002 PHE B 370 TRP 0.034 0.002 TRP E 441 HIS 0.009 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00422 (12273) covalent geometry : angle 0.61855 (16926) hydrogen bonds : bond 0.04237 ( 595) hydrogen bonds : angle 4.04844 ( 1654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 277 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7443 (m-10) REVERT: E 289 ASP cc_start: 0.7393 (t0) cc_final: 0.7135 (t0) REVERT: E 323 MET cc_start: 0.6686 (tpt) cc_final: 0.6465 (tpp) REVERT: E 342 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7239 (tm-30) REVERT: E 787 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: E 792 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7820 (mtp180) REVERT: B 259 GLU cc_start: 0.5370 (mp0) cc_final: 0.5068 (mp0) REVERT: B 265 MET cc_start: 0.8202 (ttt) cc_final: 0.7968 (ttt) REVERT: B 295 LYS cc_start: 0.7612 (ttmm) cc_final: 0.6887 (ttmm) REVERT: B 309 THR cc_start: 0.7239 (p) cc_final: 0.7004 (p) outliers start: 40 outliers final: 15 residues processed: 233 average time/residue: 0.6150 time to fit residues: 154.8064 Evaluate side-chains 228 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 129 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 133 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 63 optimal weight: 0.1980 chunk 126 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 ASN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.181024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.152349 restraints weight = 16320.571| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.76 r_work: 0.3881 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12273 Z= 0.157 Angle : 0.602 8.887 16926 Z= 0.310 Chirality : 0.039 0.178 1882 Planarity : 0.005 0.047 1937 Dihedral : 19.517 178.521 2202 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.71 % Allowed : 14.16 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.03 (0.24), residues: 1298 helix: 1.63 (0.20), residues: 702 sheet: -1.38 (0.49), residues: 90 loop : -0.18 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E1034 TYR 0.014 0.001 TYR E1227 PHE 0.015 0.001 PHE B 195 TRP 0.037 0.002 TRP E 441 HIS 0.004 0.001 HIS E1030 Details of bonding type rmsd covalent geometry : bond 0.00367 (12273) covalent geometry : angle 0.60156 (16926) hydrogen bonds : bond 0.03998 ( 595) hydrogen bonds : angle 3.95747 ( 1654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 277 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7459 (m-10) REVERT: E 289 ASP cc_start: 0.7381 (t0) cc_final: 0.7133 (t0) REVERT: E 342 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7356 (tm-30) REVERT: E 787 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: B 259 GLU cc_start: 0.5379 (mp0) cc_final: 0.4891 (mp0) REVERT: B 295 LYS cc_start: 0.7593 (ttmm) cc_final: 0.7361 (ttmm) REVERT: B 309 THR cc_start: 0.7225 (p) cc_final: 0.6990 (p) outliers start: 31 outliers final: 14 residues processed: 227 average time/residue: 0.6129 time to fit residues: 150.2202 Evaluate side-chains 221 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 237 ASP Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 133 optimal weight: 0.1980 chunk 60 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.0770 chunk 62 optimal weight: 0.6980 chunk 81 optimal weight: 0.0020 overall best weight: 0.2546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 304 GLN E 369 ASN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 HIS E 926 ASN ** E1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1096 GLN B 311 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.183190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.154535 restraints weight = 16400.016| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.77 r_work: 0.3904 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12273 Z= 0.123 Angle : 0.576 9.554 16926 Z= 0.297 Chirality : 0.037 0.184 1882 Planarity : 0.005 0.049 1937 Dihedral : 19.427 178.182 2202 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.36 % Allowed : 15.21 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.25 (0.24), residues: 1298 helix: 1.80 (0.20), residues: 704 sheet: -1.28 (0.50), residues: 90 loop : -0.06 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E1034 TYR 0.010 0.001 TYR E1227 PHE 0.018 0.001 PHE E 612 TRP 0.043 0.001 TRP E 441 HIS 0.005 0.001 HIS E 608 Details of bonding type rmsd covalent geometry : bond 0.00278 (12273) covalent geometry : angle 0.57567 (16926) hydrogen bonds : bond 0.03581 ( 595) hydrogen bonds : angle 3.83134 ( 1654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 277 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7456 (m-10) REVERT: E 342 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7389 (tm-30) REVERT: E 787 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: E 792 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7851 (mtp180) REVERT: E 1060 LEU cc_start: 0.7989 (mp) cc_final: 0.7784 (mt) REVERT: E 1128 ASP cc_start: 0.7610 (m-30) cc_final: 0.7296 (m-30) REVERT: B 259 GLU cc_start: 0.5456 (mp0) cc_final: 0.5065 (mp0) REVERT: B 265 MET cc_start: 0.7990 (ttt) cc_final: 0.7681 (tpt) REVERT: B 295 LYS cc_start: 0.7606 (ttmm) cc_final: 0.7350 (ttmm) REVERT: B 309 THR cc_start: 0.7165 (p) cc_final: 0.6936 (p) outliers start: 27 outliers final: 14 residues processed: 239 average time/residue: 0.5955 time to fit residues: 153.9005 Evaluate side-chains 231 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 1159 ASP Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain E residue 1219 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 304 GLN E 369 ASN E 528 ASN E 572 GLN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 799 ASN E 920 HIS ** E1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.180481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.151324 restraints weight = 16333.915| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.78 r_work: 0.3870 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12273 Z= 0.184 Angle : 0.636 10.348 16926 Z= 0.324 Chirality : 0.041 0.178 1882 Planarity : 0.005 0.055 1937 Dihedral : 19.427 179.112 2202 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.80 % Allowed : 15.73 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.05 (0.24), residues: 1298 helix: 1.63 (0.20), residues: 703 sheet: -1.41 (0.51), residues: 84 loop : -0.16 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E1034 TYR 0.015 0.001 TYR E1227 PHE 0.013 0.002 PHE E 612 TRP 0.037 0.002 TRP E 441 HIS 0.006 0.001 HIS E 608 Details of bonding type rmsd covalent geometry : bond 0.00435 (12273) covalent geometry : angle 0.63601 (16926) hydrogen bonds : bond 0.04095 ( 595) hydrogen bonds : angle 3.95896 ( 1654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 277 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7434 (m-10) REVERT: E 342 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7137 (tm-30) REVERT: E 787 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: B 259 GLU cc_start: 0.5558 (mp0) cc_final: 0.5134 (mp0) REVERT: B 265 MET cc_start: 0.8169 (ttt) cc_final: 0.7890 (tpt) REVERT: B 295 LYS cc_start: 0.7601 (ttmm) cc_final: 0.7361 (ttmm) REVERT: B 301 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6836 (mmt) REVERT: B 309 THR cc_start: 0.7322 (p) cc_final: 0.7088 (p) outliers start: 32 outliers final: 17 residues processed: 232 average time/residue: 0.6008 time to fit residues: 150.8725 Evaluate side-chains 236 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 96 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 304 GLN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 528 ASN ** E 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 847 ASN E 920 HIS ** E1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.180896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.152139 restraints weight = 16325.863| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.77 r_work: 0.3871 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12273 Z= 0.165 Angle : 0.630 10.631 16926 Z= 0.323 Chirality : 0.040 0.182 1882 Planarity : 0.005 0.058 1937 Dihedral : 19.364 178.411 2200 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.19 % Allowed : 16.70 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.04 (0.24), residues: 1298 helix: 1.63 (0.20), residues: 703 sheet: -1.50 (0.50), residues: 84 loop : -0.16 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E1034 TYR 0.013 0.001 TYR E1227 PHE 0.009 0.001 PHE E1146 TRP 0.052 0.002 TRP E 441 HIS 0.006 0.001 HIS E 930 Details of bonding type rmsd covalent geometry : bond 0.00388 (12273) covalent geometry : angle 0.63036 (16926) hydrogen bonds : bond 0.03965 ( 595) hydrogen bonds : angle 3.97016 ( 1654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 296 LEU cc_start: 0.7970 (mt) cc_final: 0.7720 (tt) REVERT: E 342 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 259 GLU cc_start: 0.5564 (mp0) cc_final: 0.5142 (mp0) REVERT: B 295 LYS cc_start: 0.7614 (ttmm) cc_final: 0.7383 (ttmm) REVERT: B 309 THR cc_start: 0.7266 (p) cc_final: 0.7030 (p) outliers start: 25 outliers final: 15 residues processed: 226 average time/residue: 0.6007 time to fit residues: 146.8388 Evaluate side-chains 225 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 119 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 304 GLN ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 528 ASN ** E 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 847 ASN E 920 HIS ** E1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.180225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.151238 restraints weight = 16469.904| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.78 r_work: 0.3861 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12273 Z= 0.179 Angle : 0.645 10.443 16926 Z= 0.331 Chirality : 0.041 0.180 1882 Planarity : 0.005 0.062 1937 Dihedral : 19.349 178.492 2200 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.10 % Allowed : 17.13 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.00 (0.24), residues: 1298 helix: 1.60 (0.20), residues: 703 sheet: -1.59 (0.49), residues: 84 loop : -0.16 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E1034 TYR 0.014 0.001 TYR E1227 PHE 0.015 0.002 PHE B 195 TRP 0.049 0.002 TRP E 441 HIS 0.007 0.001 HIS E 930 Details of bonding type rmsd covalent geometry : bond 0.00424 (12273) covalent geometry : angle 0.64538 (16926) hydrogen bonds : bond 0.04078 ( 595) hydrogen bonds : angle 4.00353 ( 1654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 296 LEU cc_start: 0.7959 (mt) cc_final: 0.7747 (tt) REVERT: E 342 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7347 (tm-30) REVERT: E 616 GLN cc_start: 0.7350 (mt0) cc_final: 0.6955 (mt0) REVERT: E 792 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7875 (mtp180) REVERT: B 259 GLU cc_start: 0.5642 (mp0) cc_final: 0.5212 (mp0) REVERT: B 265 MET cc_start: 0.8210 (ttm) cc_final: 0.7607 (tpt) REVERT: B 295 LYS cc_start: 0.7625 (ttmm) cc_final: 0.6838 (ttmm) REVERT: B 309 THR cc_start: 0.7343 (p) cc_final: 0.7098 (p) outliers start: 24 outliers final: 15 residues processed: 221 average time/residue: 0.6265 time to fit residues: 149.5068 Evaluate side-chains 225 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 792 ARG Chi-restraints excluded: chain E residue 1192 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 84 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 88 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 528 ASN ** E 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 847 ASN E 920 HIS ** E1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.181055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.152311 restraints weight = 16270.734| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.76 r_work: 0.3880 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12273 Z= 0.162 Angle : 0.641 9.852 16926 Z= 0.329 Chirality : 0.040 0.179 1882 Planarity : 0.006 0.063 1937 Dihedral : 19.312 178.173 2200 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.10 % Allowed : 17.22 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.02 (0.24), residues: 1298 helix: 1.63 (0.20), residues: 703 sheet: -1.73 (0.48), residues: 84 loop : -0.15 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E1034 TYR 0.013 0.001 TYR E1227 PHE 0.015 0.001 PHE B 195 TRP 0.048 0.002 TRP E 441 HIS 0.011 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00382 (12273) covalent geometry : angle 0.64070 (16926) hydrogen bonds : bond 0.03956 ( 595) hydrogen bonds : angle 3.99802 ( 1654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5310.30 seconds wall clock time: 90 minutes 53.09 seconds (5453.09 seconds total)